WISARD[wɪzərd]
Workbench for Integrated Superfast Association study with Related Data
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Case tutorial

  1. Study design
  2. Data management
  3. Summary statistics
  4. Association analysis
  5. Miscellaneous
 

List of Options

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Categories [top]

  • Input related
  • Output control related
  • Execution related
  • Additional output related
  • Sample structure related
  • Interaction analysis related
  • Estimation/compensation related
  • Filtering related
  • Gene-set analysis related
  • Single analysis related
  • Genetic summary related
  • Miscellaneous

    • Description [top]

    Full name Shortcut Default Format

    Input related
    --bed -j NULL file path
    Assigns input with PLINK Binary PED format. It is recommended to give full path with extension(.bed), but the extension can be omitted if an extension is bed.
  • Can't use with : --vcf,--bcf,--ped,--tped,--dosage,--simtrio,--lgen,--simfam
    		•
    --ped -i NULL file path
    Assigns input with one of PED/RAW format, full path of PED file with extension required
  • Can't use with : --vcf,--bcf,--bed,--tped,--dosage,--simtrio,--lgen,--simfam
  • Can use with : --map,--nomap,--indel,--acgt,--1234,--sepallele,--consecallele,--nskip
    		•
    --tped -tp NULL file path
    Assigns input with transposed PED format, full path of TPED file is required
  • Can't use with : --vcf,--bcf,--ped,--dosage,--bed,--simtrio,--lgen,--simfam
    		•
    --lgen -l NULL file path
    Assigns input with long format, full path of LGEN file with extension required
  • Can't use with : --ped,--vcf,--bcf,--bed,--tped,--dosage,--simtrio,--simfam
  • Can use with : --map,--fam,--indel,--acgt,--1234,--sepallele,--consecallele,--nskip
    		•
    --dosage -d NULL file path
    Assign input with dosage data, data type will be automatically determined. Full path of dosage data file with extension required
  • Can't use with : --vcf,--bcf,--ped,--tped,--bed,--simtrio,--lgen,--simfam
    		•
    --map -M NULL file path
    Use assigned path to load map file when PED file has assigned as an input
  • Must use with : --ped/--lgen
    		•
    --bim -bi NULL file path
    Use assigned path to load bim file when BED file has assigned as an input
  • Must use with : --bed
    		•
    --fam -F NULL file path
    Use assigned path to load fam file when BED file has assigned as an input
  • Can use with : --bed/--tped/--lgen/--simfam/--vcf
    		•
    --bcf -B NULL File path
    Retrieve BCF file as an input
  • Can't use with : --vcf,--tped,--ped,--dosage,--bed,--simtrio,--lgen,--simfam,--variantvar
  • Can use with : --filqual,--vcfqc
    		•
    --vcf -V NULL file path
    Assign input with VCF file
  • Can't use with : --bcf,--tped,--ped,--dosage,--bed,--simtrio,--lgen,--simfam,--variantvar
  • Can use with : --filqual,--vcfqc
    		•
    --expression -EX NULL OT_STRING
    Expression input file prefix
  • Can't use with :
  • Must use with :
    • NULL No argument need
    Generate input by simulation, under given pedigree structure
  • Can't use with : --tped,--ped,--dosage,--bed,--vcf,--lgen,--simtrio
    		•
    --nsig -nx 0 positive integer
    While the generation of simulated data, set the number of 'statistically' significant variants.
  • Must use with : --simfam
    		•
    --maf -ma NULL range (0~0.5]
    Pre-defined MAF
  • Can't use with :
  • Must use with :
    • --simfreq -sq 0 file path
    Use background MAF distribution to simulate dataset.
    --mafvar -ms NULL file path
    Background MAF distribution file for the simulation of variants
  • Must use with : --simfam/--simtrio
    		•
    --extfam -sE 0 No argument need
    Let --simfam to generate extended family dataset, that one family consists of ten members.
  • Must use with : --simfam
    		•
    --trio -sT 0 No argument need
    Let --simfam to generate trio-based family dataset.
  • Must use with : --simfam
    		•
    --sampvar -h NULL file path
    Load an alternative phenotype that alternates phenotype included in input, using assigned path
  • Can't use with : --simtrio
    		•
    --nosampvarhdr -nh NULL No argument need
    Assume that there is NO header in the file assigned with --sampvar
  • Must use with : --sampvar
    		•
    --sepid -Si NULL OT_STRING
    Assume there is a separator between FID and IID rather than whitespace
  • Can't use with :
  • Must use with :
    • --pname -n * string (comma[,] separated)
    Enumrate phenotype names that will be used in the analysis, comma(,) is a separator when the case of assignment of multiple phenotypes, and star(*) is an indicator that all phenotypes in the alternative phenotype file are used
  • Must use with : --sampvar
    		•
    --cname -cn NULL string (comma[,] separated)
    Enumrate covariate names that will be used in the analysis, comma(,) is a separator when the case of assignment of multiple covariates, and star(*) is an indicator that all phenotypes in the alternative phenotype file are used
  • Must use with : --sampvar
    		•
    --fname -fc NULL Column of IDs to be factor covariate(s), divided by comma(,) w/o whitespace
    Assigns covariate(s) as factor-type. Unlike --cname, covariates in --fname always treated as factor type.
  • Must use with : --sampvar
    		•
    --baseline -bl NULL string (comma[,] separated)
    COLUMN=VALUE
    Set a baseline value of factor-type covariates, note that this assignment is only valid unless the type of assigned covariate is factor and the value should be exists in the "final" dataset, otherwise it will produce error
  • Must use with : --sampvar,--cname,[FACTOR covariates]
    		•
    --variant2cov -m2 NULL No argument need
    Apply selected variants as covariates.
    --mispheno -mh -9 string
    Set a string that indicates missing value against the phenotype included in the input, and phenotypes/covariates from the alternative phenotype file used in the analysis. Any non-whitespace sequence of ascii characters allowed.
    --misgeno -mg 0 string
    Set a character or string for the representation of "genotype missingness". Any non-whitespace sequence of ascii characters allowed.
    --set -s NULL file path
    Load a set includes gene-set definition from assigned path
  • Can't use with : --setconsec,--setoverlap
    		•
    --setconsec -xc 0 Positive integer
    Automatically generates gene-variant relationship by binding consecutive k variants.
  • Can't use with : --set
  • Can use with : --setoverlap
    		•
    --setoverlap -xv 0 OT_NUMBER
    Set the size of overlap when generating set
  • Can't use with : --set
  • Must use with : --setconsec
    		•
    --setrandom -xr NULL OT_RANGE
    Automatically generate set with random variants
  • Can't use with :
  • Must use with :
    • --setspan -sn 0 OT_NUMBER
    Gene plus-minus span for mapping variant when gene definition is ranged form
  • Can't use with :
  • Must use with :
    • --geneset -pw NULL a file path of gene-set definition
    Retrieve gene-set definition from given path, and enables gene-set-testing mode.
  • Must use with : --set
    		•
    --simtrio -xt 0 No argument need
    Alternate an input as simulated trio dataset, instead of external file
  • Can't use with : --tped,--ped,--dosage,--bed,--vcf,--lgen,--simfam
    		•
    NULL positive integer
    Set the number of families simulated
  • Can't use with : --tped,--ped,--dosage,--bed,--vcf,--lgen
  • Must use with : --simtrio,--simfam
    		•
    --szvar -z 0 positive integer
    Set the number of variants simulated
  • Must use with : --simfam
    		•
    --ignoreparent -Ip 0 No argument need
    Ignore parent field of pedigree information and treat them as founders
    --ignorefid -If 0 No argument need
    Ignore FID of pedigree information but does not ignore parent field, thus be aware of error!
    --singleparent -sP NULL OT_ONOFF
    Allow single-side parent in the retrieval of pedigree structure
  • Can't use with :
  • Must use with :
    • --noparent -np 0 No argument need
    Let WISARD to assume there is no PAT and MAT field that indicates parental relationship
  • Can't use with : --filnf,--misparent
    		•
    --nofid -Nf 0 No argument need
    Let WISARD to assume there is no FID field
    --nosex -nX 0 No argument need
    Assume there is no column for sex in the six-column mandatory pedigree definition
  • Can't use with : --filmale,--filfemale,--filnosex
    		•
    --nopheno -nP 0 No argument need
    Assume there is no column for phenotype in the six-column mandatory pedigree definition
    --nasamp -xs NULL Single IID or multiple IIDs separated by comma(,) white no whitespace
    Blow out the genotype of chosen samples, can be file path containing FID & IID pair or list of IIDs divided by comma(,) with no whitespace.
  • Can't use with : --randnasamp
    		•
    --randnasamp -rx NULL A real number between 0 and 1, or positive integer
    If argument is integer and over 1, the number of samples are randomly chosen and blowed out their genotype. If the number is betwen 0 and 1, it interpreted as 'proportion'.
  • Can't use with : --nasamp
    		•
    --sampresize -az 0 positive integer (>0)
    Randomly resizing samples into given number.
    --passemptyline -pe NULL No argument need
    Pass any empty line when retrieving ALL inputs
    --dupnaming -dp NULL No argument need
    If some variant's name is duplicated, automatically correting the nume of sample.
    --impute -ie NULL No argument need
    Impute entire dataset according to the pedigree structure of given dataset.
    --makeimpute -mi NULL No argument need
    Export imputed dataset
  • Must use with : --impute
    		•
    --randbinpheno -rb NULL No argument need
    Generate random dichotomous phenotype and alternate if there is phenotype.
  • Can't use with : --randpheno
    		•
    --randpheno -re 1 No argument need
    Generate random continuous phenotype based on the standard normal distribution, and alternate if there is phenotype.
  • Can't use with : --randbinpheno
    		•
    --probandcol -pb NULL string with no whitespace
    Assign the column name representing proband information. Note that the default value for the column name for proband is 'PROBAND' and this name is reserved
  • Must use with : --sampvar
    		•
    --twincol -tw NULL string with no whitespace
    Assign the column name representing twin information. Twin information is an integer and each twin must have same and unique integer for them. Note that the default value for the column name for twin is 'TWIN' and this name is reserved
  • Must use with : --sampvar
    		•
    --indel -ID NULL No argument need
    Notify to WISARD that the input file have at least one indel variant. An error will be raised if --indel is not used for the dataset contains indel variant
    --split -sl 0 No argument need
    Split input dataset along with the chromosomes. Note that the variants within unmapped chromosomes will be
    --famsplit -FS NULL OT_ONOFF
    Export final dataset by FID
  • Can't use with :
  • Must use with :
    • --merge -me NULL Set of files divided by comma(,) w/o whitespace or file path
    From the 'base' dataset, load files from argument or path and merge all of them.
    --mergemode -mm 1 One of 1,2,3,4,5
    Set the proper merging strategy for the two genotyping having same variant name and its position.
  • Must use with : --merge
    		•
    --updvariant -um NULL a file path consisting 4 columns
    Update the entire variant table by currently inserted dataset.
    --updchr -uc * A file path of variants and its chromosome to be updated
    Update the chromosome of corresponding variant between original dataset and name-changing table file.
    --updname -un * A file path of variants and its new name to be updated
    Update the variant's name of corresponding variant between original dataset and name-changing table file.
    --updgdist -ud * A file path of variants and new genetic distance to be updated
    Update the genetic distance of corresponding variant between original dataset and name-changing table file.
    --updpos -up * A file path of variants and new position to be updated
    Update the actual position of corresponding variant between original dataset and name-changing table file.
    --updgeno -ug NULL A file path of genotypes to alter current dataset
    Update the entire genotype by input matrix.
    --acgt -ac NULL Four characters corresponding to A, C, G, T, respectively
    Define the allele coding in the dataset corresponding to A, C, G and T, respectively. Note that the argument of this option must be four characters.
  • Can't use with : --1234,[non-ACGT dataset]
    		•
    --1234 -zz NULL No argument need
    Assume that the genotype notation in the dataset file 1, 2, 3 and 4 are corresponding to actual genotype A, C, G and T, respectively. An error will be occurred if there is a character not 1, 2, 3, 4 nor missing genotype.
  • Can't use with : --acgt,[non-1234 dataset]
    		•
    --genofield -gf NULL String with no whitespace
    Define the name of field containing hard-coded genotype in number. When this option is assigned, a default field for recognizing genotype will be ignored.
  • Must use with : --vcf
    		•
    --nageno -Ng NULL Positive integer(number of genotypes) or real number (0,1) (proportion of genotypes)
    Generate given proportion of missingness to the dataset(if an argument is a real number between 0~1), or specific number of missing genotype to the dataset(if an argument is an integer more than 1)
    --napheno -NH NULL OT_REAL
    Make given portion or number of phenotype as missing
  • Can't use with :
  • Must use with :
    • --annogene -ag NULL A path of annotation file
    Assign the annotation of variants to WISARD and annotate variants.
    --annorange -ar 0 Positive integer
    Set the range of annotation based on the proximity of variant to the adjacent genes.
  • Must use with : --annogene
    		•
    --usemf -u 0 No argument need
    Utilizing the missing founders in the analyses.
    --phenostdize -pz NULL No argument need
    Standardize given phenotype value, by standard deviation value from final phenotype after all adjustment
  • Can't use with : --invnorm
    		•
    --invnorm -vn NULL No argument need
    Apply inverse-normalization transformation for given phenotype. Note that this option does not affects to the dichotomous phenotype and factor-type phenotype.
  • Can't use with : --phenostdize
    		•
    --nskip -nk NULL Positive integer
    Skips first k lines from main dataset file, such as .ped, .lgen, .tped files.
  • Can't use with :
  • Must use with :

    • Additional output related
    --out -o res file path
    Assigns output prefix, all outputs from WISARD will be generated with this prefix.
    --outmispheno -op -9 string with no whitespace
    Assign the value for representing missing phenotype value when export final dataset
  • Must use with : --makecov,--makeraw,--makeped,--makebed,--maketped,--makelgen,--makedom,--makerec,--makepheno
    		•
    --outcact -oc NULL Two integers separated by comma(,) w/o whitespace
    Determine character for case/control when generate dataset file from final dataset.
  • Can't use with : --out1case
  • Must use with : Export-related options
    		•
    --out1case -o1 NULL No argument need
    Determine character for case/control as 1/0 respectively, when generate dataset from final dataset. Equivalent to --outcact 1,0
  • Can't use with : --outcact
  • Must use with : Export-related options
    		•
    --outnoheader -on NULL No argument need
    When generate dataset in specific format from final dataset, do not export its header if the format includes header.
  • Must use with : --makeraw/--makedom/--makerec
    		•
    --outphenoonly -oo NULL No argument need
    When generate dataset in specific format from final dataset, only export phenotype if the format includes FID, IID, parental relationship and sex.
  • Must use with : --makeraw/--makedom/--makerec
    		•
    --pvalrange -pr NULL range (0~1)
    Export result only for those of p-values in the range
  • Must use with : [Analyses producing p-value]
    		•
    --time -ti NULL No argument need
    Report elapsed time for each result entry
  • Must use with : [Analyses for multiple entries]
    		•
    --remna -rn NULL No argument need
    From all results, remove the all NA's for main-term evaluation.
    --gz -Z NULL No argument need
    Force gzipping to all outputs for reduced output size (only working under WISARD with gzip feature)
  • Must use with : [WISARD with gzip]
    		•
    --sampleorder -sO NULL A path of file contains new sample order
    Re-ordering samples with specific order, as listed in file. Non-existing samples in the order file will be ignored.
    --variantorder -sM NULL A path of file contains new variant order
    Re-ordering variants with specific order, as listed in file. Non-existing variants in the order file will be ignored.
    --sortvariant -sv asc No argument need
    Sort the variants included in the final dataset with lexicographical order, if there is no additional parameter on this option, variants will be ordered by ascending order. Otherwise, it is possible to sort the variants by descending order by giving an additional parameter desc
  • Can't use with : --sortpos
    		•
    --sortsample -ss asc ascending order(asc) or descending order(desc)
    Sort the samples included in the final dataset with lexicographical order by their FID and IID sequentially, if there is no additional parameter on this option, samples will be ordered by ascending order. Otherwise, it is possible to sort the samples by descending order by giving an additional parameter desc
  • Can't use with : --sortiid
    		•
    --sortiid -si asc ascending order(asc) or descending order(desc)
    Sort the samples included in the final dataset with lexicographical order by their IID sequentially, if there is no additional parameter on this option, samples will be ordered by ascending order. Otherwise, it is possible to sort the samples by descending order by giving an additional parameter desc
  • Can't use with : --sortsample
    		•
    --sortpos -sp asc ascending order(asc) or descending order(desc)
    Sorting variants based on their physical position. This number
  • Can't use with : --sortvariant
    		•

    Execution related
    --verbose -vb 0 No argument need
    Produce more detailed output and verbose log
    --thread -t 1 positive integer
    Set the number of threads will be used in the analysis, the number exceeds the thread count available on the system will be adjusted to maximum number of threads.
    --rpath -rl NULL file path
    (R-compatible version only) Assign the path for R initialization, in case of this option is not assigned, WISARD will automatically search the path
  • Must use with : [WISARD with R]
    		•
    --interactive -I 0 No argument need
    Run WISARD as an interactive execution mode. Note that the arguments assigned with this option will affect
    --runas -r 0 file path
    Run WISARD based on an assigned path. Note that the arguments assigned with this option will affect regardless of duplication. Following file can be accepted as a valid input. 1) A log file produced from WISARD, 2) A file includes valid options
    --est -E NULL file path
    Load ".est" file produced from WISARD which including the output from EM-AI algorithm and utilize this information to analysis
    --chrwise -cw 0 No argument need
    Divide given input into chromosome, and perform analyses chromosome-wise. Note that the output also will be produced chromosome-wise
    --nomap -nm 0 No argument need
    Proceed analyses regardless of presence of map file, variant name and position will be assigned arbitrary, so options related to chromosome, physical position and genetic distance will not working properly
  • Must use with : --ped/--lgen
    		•
    --nopos -no 0 No argument need
    When loading variant description file for given input, assume there is no column for physical position of variant.
  • Can't use with : --nomap
    		•
    --nogdist -ng 0 No argument need
    When loading variant description file for given input, assume there is no column for genetic distance of variant.
  • Can't use with : --nomap
    		•
    --misparent -mq NULL String with no whitespace
    Determine character for the parental notation of founder. i.e., character for the parent is missing.
  • Can't use with : --noparent
    		•
    --sepallele -sa NULL Single ascii character
    Define the separator of two alleles in the genotype data. A default separator is whitespace.
  • Can't use with : --consecallele
    		•
    --consecallele -cl NULL No argument need
    Assume that two alleles are consecutive when loading genotype data.
  • Can't use with : --sepallele
    		•
    --sep -xp NULL Single ascii character
    Set the field separator for the loading of dosage file
  • Must use with : ???
    		•
    --ginv -gi 0 No argument need
    Utilize Generalized inverse method if traditional method failed.
    --seed -S NULL positive integer
    Force the random seed. Can be utilized to replication
    --nolmm -nl NULL No argument need
    Never fit linear mixed model and assumes independency across variables in the model. This option affects all analyses using linear mixed model.
    --nosysfeat -ns NULL No argument need
    Disable all system functinalities utilizing system-dependent spec.
    --natural -nt NULL No argument need
    Apply natural sort when automatically sorting variants or samples.
  • Must use with : --sortiid,--sortsample,--sortvariant
    		•
    --avail -av 0 No argument need
    Perform all analyses WITHOUT any imputation. If the analysis does not support a test without imputation, the result of that analysis for the makrer/gene having missing genotype will be NA
  • Must use with : --fqls/--qls/--regression
    		•
    --R -R NULL No argument need
    When WISARD supports R connectivity, execute user-defined R code for the customized analysis. If multiple files assigned, it will be executed sequentially.
  • Must use with : R connectivity
    		•
    --ext -X NULL file path
    Load external libraries for WISARD and execute them.
    --nodata -nd NULL No argument need
    Continus an execution although there is no genotype data. This option is required for some special analyses, which do not need any genotype data.
  • Can't use with :
  • Must use with :
    • --species -sc human No argument need
    Set the species to be analyzed. To see the list of supported species, refer this page
  • Can't use with :
  • Must use with :

    • Additional output related
    --makeped -mp 0 No argument need
    Export final dataset as PED format
    --makebed -mb 0 No argument need
    Export final dataset as BED format
    --sampmajor -sm NULL No argument need
    Export PLINK BED file with sample-major format.
  • Must use with : --makebed,--genesplit
    		•
    --makeraw -mr 0 No argument need
    Export final dataset as RAW format
    --makevcf -mv 0 No argument need
    Export final dataset as VCF format. Note that all genotypes in the dataset will be treated as unphased
    --ref -rf NULL A path of reference FASTA sequence
    Assign the reference FASTA sequence to WISARD
  • Must use with : --makevcf
    		•
    --makemdr -mM NULL OT_ONOFF
    Generates dataset file that can be accepted by MDR program, using final dataset.
  • Can't use with :
  • Must use with :
    • --makebcf -mF 0 No argument need
    Generates dataset file with binary VCF format, using final dataset.
  • Can't use with :
  • Must use with :
    • --maketped -mT 0 No argument need
    Export final dataset as transposed PED format
    --famsummary -Fs 0 No argument need
    Produce a report about the family structure based on their FID
    --ncsummary -nc 0 No argument need
    Produce a report about the nuclear families based on their pedigree structure
    --makecov -mc 0 No argument need
    Export processed and filtered covariates information to file
    --makepheno -mP 0 No argument need
    Export samples and their phenotype values in the final dataset
    --makeflag -Mf NULL OT_STRING
    Flags for generating sample-based output files
  • Can't use with :
  • Must use with :
    • --makelgen -mn NULL No argument need
    Export the final dataset as LGEN format
    --makerec -mR 0 No argument need
    Export the final dataset as recessive coding
    --makedom -mD 0 No argument need
    Export the final dataset as dominant coding
    --makemerlin -om NULL No argument need
    Convert the final dataset to the format that can be accepted in MERLIN program.
    --makebeagle -mL NULL No argument need
    Convert the final dataset to the format that can be accepted in Beagle program.
    --cosi -co NULL No argument need
    Convert the final dataset to the format that can be accepted in COSI program.
    --makegen -mG NULL No argument need
    Export the final dataset as GEN format.
    --makebgen -mB NULL No argument need
    Export the final dataset as binary GEN format.
    --zipbgen -zb NULL No argument need
    Deflate the genotype probability data of binary GEN format.
  • Must use with : --makebgen
    		•
    --makeweight -mw NULL No argument need
    Export computed/loaded weight values
    --makeset -mS NULL No argument need
    Export retrieved and matched gene-variant relationship as file, non-existing variants in final dataset or the gene does not have any existing variants will be removed.
  • Must use with : --set/--setconsec
    		•
    --settype -et 0 One of 1,2,3,4,5
    Determine the type of exported gene-variant relationship.
  • Must use with : --makeset,--set/--setconsec
    		•
    --listvariant -lm NULL No argument need
    Export the list of variants in the final dataset
    --listsample -ls NULL No argument need
    Export the list of samples in the final dataset
    --listfounder -lf NULL No argument need
    Export the list of founders in the final dataset
    --makegeno -mZ 0 No argument need
    Generate genotype file with RAW format, according to the definition of gene-variants mapping.
  • Must use with : --set/--setconsec
    		•
    --makeclgeno -mz 0 No argument need
    Perform genotype clumping based on the gene-variant mapping definition and export the clumped result
  • Must use with : --qtest
    		•
    --genesplit -GS NULL No argument need
    Split the dataset by gene-marker mapping.
  • Must use with : --set/--setconsec
    		•
    --out1234 -t1 NULL No argument need
    In the export of non-binarized format, change A/C/G/T into 1/2/3/4, respectively.
  • Can't use with : --outacgt
    		•
    --outacgt -oa NULL Four characters corresponding to A, C, G, T, respectively
    In the export of non-binarized format, change A/C/G/T into given four characters, respectively.
  • Can't use with : --out1234
    		•

    Sample structure related
    --kinship -k 0 No argument need
    Compute PDDT score matrix and substitute it as the sample correlation structure
  • Can't use with : --hybrid,--cor,--ibs,--corpearson,--indep,--ktau,--empktau,--empiall,--medcor
    		•
    --hybrid -hy 0 No argument need
    Compute hybrid score matrix and substitute it as the sample correlation structure. An element of hybrid score will have PDDT score if both samples have same FID, otherwise have empirical correlation
  • Can't use with : --ibs,--corpearson,--cor,--kinship,--indep,--ktau,--empktau,--empiall,--medcor
    		•
    --ibs -bs 0 No argument need
    Compute IBS score matrix, and substitute it as the sample correlation structure. Note that it will not working properly against rare-varaint only dataset
  • Can't use with : --hybrid,--corpearson,--cor,--pddt,--indep,--ktau,--empktau,--empiall,--medcor
    		•
    --cor -c NULL file path
    Load the sample correlation structure from assigned path, instead of computing sample correlation structure directly. Note that the number of samples in the file must match with the number of samples in the final dataset. If the assigned input is not 3-column format, the sequence of samples also must match
  • Can't use with : --hybrid,--indep,--corpearson,--pddt,--ibs,--ktau,--empktau,--empiall,--medcor
    		•
    --medcor -Mc 0 No argument need
    Compute empirical correlation based on the median of observed value, instead of mean of observed values
  • Can't use with : --hybrid,--indep,--corpearson,--pddt,--ibs,--ktau,--empktau,--empiall,--cor
    		•
    --corpearson -cp 0 No argument need
    Compute Pearson's correlation coefficient across all samples based on the genotype, and substitute it as the sample correlation matrix
  • Can't use with : --indep,--cor,--pddt,--ibs,--ktau,--empktau,--empiall,--medcor
    		•
    --hamming -hn NULL OT_ONOFF
    Calculate relatedness matrix using Hamming distance
  • Can't use with :
  • Must use with :
    • --cordiag1 -cd 0 No argument need
    Force the diagonal term of the sample correlation structure to be 1 if the value is less than 1. This option will not affect to the off-diagonal term
    --ktau -kt NULL No argument need
    Compute sample relatedness using Kendall's tau correlation coefficient, raw genotype used
  • Can't use with : --ibs,--corpearson,--cor,--kinship,--indep,--hybrid,--empktau,--empiall,--medcor
    		•
    --empktau -ek NULL No argument need
    Compute sample relatedness using Kendall's tau correlation coefficient, normalized genotype used
  • Can't use with : --ibs,--corpearson,--cor,--kinship,--indep,--hybrid,--ktau,--empiall,--medcor
    		•
    --empiall -ea NULL No argument need
    Compute empirical kinship matrix, with all available samples instead of founder samples
  • Can't use with : --hybrid,--corpearson,--cor,--pddt,--ibs,--ktau,--empktau,--indep,--medcor
    		•
    NULL No argument need
    Perform the analyses with utilization of missing-founders, which are not included in the dataset but in the pedigree structure
    --indep -id NULL No argument need
    Force all samples in the dataset to be independent, i.e., make the sample correlation structure to identity matrix
  • Can't use with : --hybrid,--corpearson,--cor,--pddt,--ibs,--ktau,--empktau,--empiall,--medcor
    		•
    --corpair -ca 0 No argument need
    Export sample relatedness matrix as paried form. One line consists of IIDs of two samples and their relaedness value
    --corgrm -cg 0 No argument need
    Export sample relatedness matrix with binarized GRM format used in GCTA.
  • Can't use with : --corpair
    		•
    --corepacts -ep NULL OT_ONOFF
    Export sample relatedness matrix with EPACTS kin format
  • Can't use with :
  • Must use with :
    • --x -x 0 No argument need
    Compute PDDT with an assumption of X chromosome
  • Must use with : --pddt
    		•
    --x2 -x2 0 No argument need
    Compute the theoretical kinship coefficient under X chromosome assmption(with --kinship) or convert empirical sample relatedness matrix with autosomes into X chromosome-compatible sample relatedness matrix for the statistics of X-chromosome.
  • Can't use with : --x
    		•
    NULL range (0~1)
    Determine the range of MAF to be incorporated to empirical correlation computation
  • Can use with : --ibs/--corpearson/--ktau/--empktau/--empiall/--medcor
    		•
    --makecor -MC default No argument need
    Export computed/imported sample relatedness matrix
    --makeev -mV NULL No argument need
    Export the result of eigendecomposition, consists of eigenvectors and eigenvalues.
    --ev -ev NULL File path of pre-computed eigendecomposition, w/o extension
    Load pre-computed eigendecomposition, instead of compute it.

    Interaction analysis related
    --gxe -gx 0 No argument need
    In the regression analysis, include additional covariates that regarding an interaction between genotype and given covariates
  • Must use with : --regression
    		•
    --gxecovs -gc NULL string
    Determine the columns names to investigate GxE effect. Note that the columns included in here MUST BE a subset of --cname
  • Must use with : --gxe
    		•
    --mdr -md 0 No argument need
    Perform Multifactor Dimensionality Reductionanalysis
  • Can use with : --order,--top,--mdrthr,--cv,--loocv
    		•
    --order -O 1 positive integer
    Assigne the order of interaction in MDRanalysis
  • Must use with : --mdr
    		•
    --top -T 1000 positive integer
    Report top N results based on the balanced accuracy in MDRanalysis, rather than report all results
  • Must use with : --mdr
    		•
    --hmdr -hm NULL No argument need
    Perform Hierarchical MDRanalysis (unimplemented)
    --fuzzymdr -zm NULL OT_ONOFF
    Perform fuzzy MDR analysis
  • Can't use with :
  • Must use with :
    • --gmdr -gd NULL No argument need
    Perform Generalized MDR analysis for quickly finding Gene-Gene interaction for continuous phenotype.
    --boost -bo NULL No argument need
    Perform BOOST analysis for quickly finding Gene-Gene interaction.
    --thrboost -Bt 30 Positive real number
    Determine the reporting threshold for BOOST analysis.
  • Must use with : --boost
    		•
    --quickepi -qe NULL No argument need
    Perform the fast-epistasis analysis proposed in PLINK
    --genemdr -Gm NULL No argument need
    Perform Gene-based MDR.
  • Must use with : --set
    		•
    --mdrthr -dt NULL Real value ranged (0,1]
    MDR reporting threshold
  • Must use with : --mdr
    		•
    --cv -cv NULL Positive integer > 1
    Performs k-fold cross-validation in the analysis.
  • Can't use with : --loocv
  • Must use with : --mdr
    		•
    --loocv -lv NULL No argument need
    Performs Leave-one-out cross-validation (LOOCV) in the analysis.
  • Can't use with : --cv
  • Must use with : --mdr
    		•
    --hmdr -hm NULL No argument need
    Perform Hierarchical MDRanalysis (unimplemented)
    --hmdrprior -hp 1 OT_STRING
    Give priors to HMDR analysis
  • Can't use with :
  • Must use with :

    • Estimation/compensation related
    --emcount -ec 5 positive integer
    Determine the count of EM iteration in the analysis using EM-AI algorithm
  • Must use with : --scoretest/--heritability
    		•
    --aithr -at 1e-8 real number (0~1)
    Determine the convergence threshold of AI iteration in the analysis using EM-AI algorithm
  • Must use with : --scoretest/--heritability
    		•
    --nostop -xx 0 No argument need
    Do not break up AI iteration until the convergence threshold is satisfied in AI algorithm
  • Must use with : --scoretest/--heritability
    		•
    --blup -b NULL file path
    In case of determining phenotype, set the final phenotype value as the subtraction from given phenotype to BLUP value in the assigned path. Note that the dataset used to compute BLUP and target dataset should be identical, and also if the given phenotype is dichotomous(binary) phenotype, it will be considered as continuous phenotype
  • Can use with : --scoretest/--heritability/--gmdr
    		•
    --ml -ml 0 No argument need
    Use ML(Maximum likelihood) method instead of REML(REstricted Maximum Likelihood) method, when perform score test. Some score tests that REML cannot be applied will automatically use ML method regardless of the presence of this option
  • Must use with : --scoretest/--heritability/--gemma
    		•
    --specdcmp -sd 0 No argument need
    Use spectral decomposition method instead of EM-AI algorithm in the analyses utilizing Linear Mixed Model
  • Can't use with : --nospecdcmp
  • Must use with : --scoretest/--heritability
    		•
    --nospecdcmp -ne NULL No argument need
    Do not perform the spectral decomposition in any circumtances.
  • Can't use with : --specdcmp
    		•
    --makeblup -mu 0 No argument need
    Export BLUP value of all given phenotypes after LMM fitting
  • Must use with : --scoretest/--heritability
    		•
    --heritability -he 0 No argument need
    Perform the analysis of estimated heritability based on the phenotypes and given family structure
    --powercalc -pl 0 No argument need
    Perform the analysis of expected statistical power under given conditions
    --powercalc2 -px 0 No argument need
    Perform the analysis of expected statistical power under given conditions
    --noshuffle -Nh 0 No argument need
    (For validation purpose) Do not shuffle the phenotype information when perform expected power estimation analysis
  • Must use with : --powercalc
    		•
    --nperm -Ne 1000 positive integer
    Set the number of permutations for the analyses using permutation scheme
  • Must use with : --powercalc
    		•
    --permfile -PF NULL OT_STRING
    User-defined permutations to perform, by sample IIDs
  • Can't use with :
  • Must use with :
    • --seqperm -SP NULL OT_STRING
    Sequence of permutations to perform
  • Can't use with :
  • Must use with :
    • --npheno -Np 0 positive integer
    Assign the number phenotypes for the analysis of expected power estimation
  • Must use with : --powercalc
    		•
    --nsamp -Ns 0 positive integer
    Assign the number of samples for the analysis of expected power estimation
  • Must use with : --powercalc
    		•
    --rho -rh 0 real number (-1~1)
    Assign the prior correlation for the analysis of expected power estimation
  • Must use with : --powercalc
    		•
    --rhopheno -rp 0 real number (-1~1)
    Assign the prior correlation among phenotypes for the analysis of expected power estimation
  • Must use with : --powercalc
    		•
    --heri -hi 0 real number (0~1)
    Assign the prior heritability for the analysis of expected power estimation
  • Must use with : --powercalc
    		•
    --beta -be 0 real number
    Assign the effect of case-control differenc(beta) for the analysis of expected power estimation
  • Must use with : --powercalc
    		•
    --sxa -xa NULL No argument need
    Perform sample selection analysis from given pedigree structure.

    Filtering related
    NULL range (0~1)
    Exclude all variants satisfying the condition that the MAF is in specified range
  • Can't use with : --incfreq
  • Must use with : --freq,--freq≠corr
  • Can use with : --window
    		•
    NULL range (0~1)
    Include the variants that satisfying its MAF in given range only to the analyses
  • Can't use with : --filfreq
    		•
    --filhwe -fh NULL range (0~1)
    Exclude all variants having its p-value of Hardy-Weinberg Equilibrium test in specified range
  • Can't use with : --inchwe
  • Must use with : --hwe,--hwe≠corr
  • Can use with : --window
    		•
    --inchwe -ih NULL range (0~1)
    Include the variants to the analyses only that having its p-value of Hardy-Weinberg Equilibrium test in specified range
  • Can't use with : --filhwe
    		•
    --filvariant -fk NULL expression
    Filtering out variants which satisfies given condition. Conditions must be valid for the fields in VCF file or variant variable file.
  • Can't use with : --incvariant
  • Must use with : --variantvar/--vcf
    		•
    --incvariant -ik NULL expression
    Retrieving only the variants which satisfies given condition. Conditions must be valid for the fields in VCF file or variant variable file.
  • Can't use with : --filvariant
  • Must use with : --variantvar/--vcf
    		•
    --filgeno -fj NULL expression
    Filtering out genotypes which satisfies given condition. Conditions must be valid for the fields in VCF file.
  • Can't use with : --incgeno
  • Must use with : --vcf
    		•
    --incgeno -ij NULL expression
    Retrieving only the genotypes which satisfies given condition. Conditions must be valid for the fields in VCF file.
  • Can't use with : --filgeno
  • Must use with : --vcf
    		•
    --filgind -fg NULL range (0~1)
    Exclude all samples having its genotyping rate in specified range
  • Can't use with : --incgind
    		•
    --incgind -ig NULL range (0~1)
    Include only the samples having its genotyping rate in speicifed range
  • Can't use with : --filgind
    		•
    --filmac -fm NULL range (0~1)
    Exclude all variants having its number of minor alleles in specified range
  • Can't use with : --incmac
  • Can use with : --window
    		•
    --incmac -im NULL range (0~1)
    Include only the variants having its number of minor alleles in specified range
  • Can't use with : --filmac
    		•
    --filgvar -fp NULL range (0~1)
    Exclude all variants having its genotyping rate in specified range
  • Can't use with : --incgvar
  • Can use with : --window
    		•
    --incgvar -iv NULL range (0~1)
    Include only the variants having its genotyping rate in specified range
  • Can't use with : --filgvar
    		•
    --filqual -fq NULL Positive integer
    Filtering variants having its QUAL value in VCF within specific range.
  • Can't use with : --incqual
  • Must use with : --vcf/--bcf
  • Can use with : --window
    		•
    --incqual -iq NULL Positive integer
    Selecting variants having its QUAL value in VCF within specific range.
  • Can't use with : --filqual
  • Must use with : --vcf
    		•
    --filmendelfam -rF NULL Family IDs divided by comma(,) w/o whitespace or file path
    Filtering samples having their family-level Mendelian error rate is within specific range.
  • Can't use with : --incmendelfam
    		•
    --incmendelfam -xF NULL Family IDs divided by comma(,) w/o whitespace or file path
    Including samples having their family-level Mendelian error rate is within specific range.
  • Can't use with : --filmendelfam
    		•
    --filmendelsamp -rS NULL Individual IDs divided by comma(,) w/o whitespace or file path
    Filtering samples having its Mendelian error rate is within specific range.
  • Can't use with : --incmendelsamp
    		•
    --incmendelsamp -xS NULL Individual IDs divided by comma(,) w/o whitespace or file path
    Including samples having its Mendelian error rate is within specific range.
  • Can't use with : --filmendelsamp
    		•
    --filmendelvar -ds NULL Variant identifiers divided by comma(,) w/o whitespace or file path
    Filtering variants having its Mendelian error rate is within specific range.
  • Can't use with : --incmendelvar
    		•
    --incmendelvar -xm NULL Variant identifiers divided by comma(,) w/o whitespace or file path
    Including variants having its Mendelian error rate is within specific range.
  • Can't use with : --filmendelvar
    		•
    --remsamp -ir NULL file path
    Exclude all samples listed in the assigned file from the analyses, based on the pair of FID and IID, or IID only
  • Can't use with : --selsamp
    		•
    --selsamp -is NULL file path
    Include only the samples listed in the assigned file from the analyses, based on the pair of FID and IID, or IID only
  • Can't use with : --remsamp
    		•
    --remvariant -sr NULL Variant IDs divided by comma(,) w/o whitespace or file path
    Removing variants in the dataset from the argument, or from the given file.
  • Can't use with : --nomap
    		•
    --selvariant -Ss NULL Variant IDs divided by comma(,) w/o whitespace or file path
    Selecting variants in the dataset from the argument, or from the given file.
  • Can't use with : --nomap
    		•
    --filsample -fn NULL expression
    Filtering out all samples satisfying given condition. The condition should be a valid expression for sample variable.
  • Can't use with : --incsample
  • Must use with : --sampvar
    		•
    --incsample -in NULL expression
    Selecting samples only satisfying given condition. The condition should be a valid expression for sample variable.
  • Can't use with : --filsample
  • Must use with : --sampvar
    		•
    --remfam -fF 0 FIDs(divided by comma[,]) or file path
    Exclude all samples having its FID in the argument. Argument can be the path of file contains FIDs to be included, or FIDs divided by comma[,] with no whitespaces
    --selfam -iF 0 FIDs(divided by comma[,]) or file path
    Include only the samples having its FID in the argument. Argument can be the path of file contains FIDs to be included, or FIDs divided by comma[,] with no whitespaces
    --filrange -rr NULL a path of file consisting 3 columns(chromosome, start, end)
    Filtering out variant if the physical position of variant resides in given range in the file.
  • Can't use with : --nomap
    		•
    --incrange -rs NULL a path of file consisting 3 columns(chromosome, start, end)
    Selecting only variants if the physical position of variant resides in given range in the file.
  • Can't use with : --nomap
    		•
    --chr -ch NULL 1~22, X, Y
    Include only the chromosomes listed in the argument, an assignment of multiple chromosomes should be divided with comma(,) with no space. Note that using of --autoonly with this option with arguments including sex chromosomes will produce error
  • Can't use with : --nomap
    		•
    --autoonly -U 0 No argument need
    Include only the autosomes in the analyses, i.e., exclude all non-autosome variants including unmapped and sex chromosome variants
  • Can't use with : --sexonly,--nomap
    		•
    --sexonly -sx 0 No argument need
    Includy only the sex chromosomes in the analyses, i.e., exclude all non-sex chromosome variants
  • Can't use with : --autoonly
    		•
    --snvonly -vo 0 No argument need
    Filtering out all variants if they are not SNV. i.e., filtering out the makrer if its major/minor allele is not a locus
  • Can't use with : --indelonly
    		•
    --indelonly -xo 0 No argument need
    Filtering out all variants if they are SNV. i.e., filtering out the variant if its major and minor allele are all a single locus.
  • Can't use with : --snvonly[RAW file]
    		•
    --phasedonly -po 0 No argument need
    In the loading of VCF file, remove out all genotypes except fo properly phased genotype.
  • Can't use with : --unphasedonly
  • Must use with : --vcf
    		•
    --unphasedonly -uo 0 No argument need
    In the loading of VCF file, remove out all genotypes except fo properly unphased genotype.
  • Can't use with : --phasedonly
  • Must use with : --vcf
    		•
    --1case -x1 0 No argument need
    Change an indicator of binary phenotype from default, 2(case)/1(control) to 1(case)/0(control)
  • Can't use with : --cact
    		•
    --cact -cc NULL two integers separated by comma(,) with no whitespace
    Sequentially assign two integer value represents case and control phenotype, respectively. Only the two integers divided by comma[,] with NO whitespaces are allowed.
  • Can't use with : --1case
    		•
    --1sex -s1 0 No argument need
    Set 1=female and 0=male for sex coding.
  • Can't use with : --mafe
    		•
    --mafe -MF NULL Two strings separated with comma(,) with no whitespaces
    Set male and female coding for input, respectively.
  • Can't use with : --1sex
    		•
    --varresize -sz 0 Positive integer(number of variants) or real number (0,1) (proportion of variants)
    Resizing the number of variants in the dataset by randomly selecting variants. When the argument is positive integer, corresponding number of variants will be chosen. Otherwise the argument is real number between 0 and 1, corresponding proportion of variants will be chosen.
    --vcfqc -vq 0 No argument need
    Retrieve only the makers having its variant quality is PASS when process VCF input
  • Must use with : --vcf/--bcf
    		•
    --filnf -fN 0 No argument need
    Exclude all non-founder samples from analyses
  • Can't use with : --nofam,--noparent
    		•
    --filmf -fs 0 No argument need
    Filtering out all missing founder samples from the analyses
    --filcase -fa 0 No argument need
    Exclude case samples from analyses
  • Must use with : [Binary trait]
    		•
    --filcontrol -ft 0 No argument need
    Exclude control samples from analyses
  • Must use with : [Binary trait]
    		•
    NULL string
    Filtering samples based on the condition related to phenotype
  • Can't use with : --incpheno
  • Can use with : --sampvar,--pname
    		•
    NULL string expression
    Like --filpheno, filtering out samples that satisfying specific condition on their covariates
  • Can't use with : --inccov
  • Must use with : --pheno,--cname
    		•
    NULL string expression
    Include only the samples satisfying the condition related to phenotype
  • Can't use with : --filpheno
  • Can use with : --pheno,--pname
    		•
    NULL string expression
    Like --filcov, include only the samples that satisfying specific condition on their covariates
  • Can't use with : --filcov
  • Must use with : --pheno,--cname
    		•
    --regex -er NULL OT_ONOFF
    Use regular expression in the acceptable options
  • Can't use with :
  • Must use with :
    • --filgdist -fi NULL range
    Exclude all variants satisfying the condition that its genetic distance in given range
  • Can't use with : --incgdist,--nomap
  • Can use with : --window
    		•
    --incgdist -ii NULL range
    Include only the variants satisfying the condition that its genetic distance in given range
  • Can't use with : --filgdist,--nomap
    		•
    --filmale -fl 0 No argument need
    Exclude all male samples from subsequent analyses
    --filfemale -fe 0 No argument need
    Exclude all female samples from subsequent analyses
    --filnosex -fx 0 No argument need
    Exclude all samples who missing their sex information
    --filmispheno -fo 0 No argument need
    Filtering out all samples having missing phenotype. If there are alternative phenotype or multiple phenotype, all samples having AT LEAST one missing will be filtered out.
    --founderonly -Fo 0 No argument need
    Using only founder samples in LD computation and sample relatedness estimation
    --filgenic -fG NULL No argument need
    Filtering out all of variants do not reside in genic region, based on the gene range file.
  • Can't use with : --filintergenic
    		•
    --filintergenic -fI NULL No argument need
    Filtering out all of variants do not reside in intergenic region, based on the gene range file.
  • Can't use with : --filgenic
    		•
    --incmistest -iM NULL range (0~1)
    Include variants only having its p-value of random missingness test from case-control data is within range
  • Can't use with : --filmistest
  • Must use with : --mistest
    		•
    --filmistest -fM NULL range (0~1)
    Exclude variants having its p-value of random missingness test from case-control data is within range
  • Can't use with : --incmistest
  • Must use with : --mistest
    		•
    --filtreport -fr NULL No argument need
    Write out a report for the filtered-out samples about which reason was they have filtered out.

    Gene-set analysis related
    --genetest -tg NULL No argument need
    Perform basic two gene-level test (CMC and Collapsing method)
  • Must use with : --set/--setconsec
    		•
    --logistic -lg 0 No argument need
    Performs gene-level test after the fitting of logistic regression model under the assumption of unrelated dataset
  • Must use with : --genetest
    		•
    --imputepheno -ip 0 No argument need
    Substitute the phenotype to 0 if it is missing, just in case of gene-level analysis of dichotomous univariate phenotype with the assignment of --prevalence
    --skat -sk 0 No argument need
    Perform SKAT test, in addition to --genetest
  • Must use with : --genetest
    		•
    --farvat -Fv 0 No argument need
    Perform FARVAT analysis for gene-level association test.
  • Must use with : --set/--setconsec
    		•
    --farvatx -Fx 0 OT_ONOFF
    Perform FARVATX analysis
  • Can't use with :
  • Must use with :
    • --farvatxd -Fd 0.5 OT_REAL
    Assumed D in FARVATX analysis
  • Can't use with :
  • Must use with :
    • --farvatxndiv -Xv 5 OT_NUMBER
    Number of divisions for FARVATX test
  • Can't use with :
  • Must use with :
    • --pedgene -pg 0 OT_ONOFF
    Perform pedgene analysis
  • Can't use with :
  • Must use with :
    • --pedcmc -pc 0 No argument need
    Perform PedCMC test, in addition to --genetest
  • Must use with : --genetest
    		•
    --raremaf -rm 0.01 real number (0~1)
    Set the MAF threshold divides rare/common of variant when doing --pedcmc
  • Must use with : --pedcmc
    		•
    --genesummary -sg 0 No argument need
    Export brief summary for gene-variant corresponding result
  • Must use with : --set/--setconsec
    		•
    --gmapsummary -xg 0 No argument need
    Export gene-variant mapping status.
  • Must use with : --set
    		•
    --genesize -gr NULL range (positive integer)
    Exclude all gene definitions do not satifies its number of variants included in gene definition
  • Can't use with : --setconsec
  • Must use with : --set
    		•
    --gsmacthr -gt 0 positive integer
    Exclude all gene definitions do not satifies its sum of minor allele count(MAC) from the variants included
  • Must use with : --genetest
    		•
    --skato -so 0 No argument need
    Perform SKAT-o test, in addition to --genetest
  • Must use with : --genetest
    		•
    --skatondiv -ov 0 Positive integer (>=2)
    Set the number of division for the SKAT-o test.The size of each division is fixed to 1/(#division-2).
  • Can't use with : --skatodivs
  • Must use with : --skato
    		•
    --skatodivs -oz NULL Values ranged [0,1], separated with comma(,) with no whitespace
    Set the user-defined rho values for SKAT-o computation.
  • Can't use with : --skatondiv
  • Must use with : --skato
    		•
    --longitudinal -L NULL file path
    Perform gene-level test based against longitudinal phenotype
  • Can't use with : --mfhom,--mfhet
  • Must use with : --genetest,--sampvar,--pname,--set/--setconsec
    		•
    --noweight -ew 0 No argument need
    Let the analyses using variant-level weight do not apply weights.
  • Can't use with : --weight,--mafweight,--betaweight
    		•
    --betaweight -bw 1,25 No argument need
    Automatically generate a weight for variant based on the distribution of beta(1, 25)
  • Can't use with : --weight,--mafweight,--equalweight
    		•
    --mafweight -Mw 0 No argument need
    Apply MAF-based inverse weight for all analyses requiring variant-wise weight.
  • Can't use with : --weight,--betaweight,--noweight
    		•
    --weight -w NULL file path
    Load user-defined weights. No missing or duplicated weight is allowed.
  • Can't use with : --equalweight,--betaweight,--mafweight
    		•
    --prevalence -pv NULL real number(0~1),two real number(0~1),multiple real number(0~1)
    Set the prevalence of disease, for the analyses requiring that. Two prevalences separated comma(,) with no whitespace are allowed in univariate case, to assign separate prevalences for male and female, respectively. In case of multivariate case, the number of prevalences MUST be same with the number of phenotypes analyzed.
  • Must use with : --genetest/--fqls
    		•
    --qtest -Q 0 No argument need
    Perform Q-test analysis
  • Must use with : --set/--setconsec
    		•
    --qtestclump -Qc 0 No argument need
    Clumping highly-correlated variants into single column when performing Q-test
  • Must use with : --qtest
    		•
    NULL range (0~1)
    Define the range of variant's MAF to performing Q-test
  • Must use with : --qtest
    		•
    --qteststt -Qs 0.2 range (0~1)
    Adjust soft truncation threshold for Q-test.
  • Must use with : --qtest
    		•
    --qtestbetacov -Qb 0 No argument need
    Export a variance-covariance of beta estimates for each gene-level test when perform Q-test.
  • Must use with : --qtest
    		•
    --makebeta -aa 0 No argument need
    Export beta estimates in Q-test
  • Must use with : --qtest
    		•
    --vt -vt 0 No argument need
    Perform Variable-Threshold test
  • Must use with : --genetest
    		•
    --kbac -K 0 No argument need
    Perform gene-level test using KBAC statistic proposed by Liu et al.
  • Must use with : --genetest
    		•
    --kbacalpha -ka 0.05 No argument need
    Setting alpha level of KBAC test
  • Must use with : --kbac
    		•
    --kbac2side -k2 0 No argument need
    Performing 2-sided test and 1-sided test simultaneously in KBAC test.
  • Must use with : --kbac
    		•
    --kbackernel -kk hypergeometric No argument need
    Change the kernel of KBAC test.
  • Must use with : --kbac
    		•
    --wsum -ws 0 No argument need
    Perform gene-level test using Weighted Sum statistic proposed by Madsen et al.
  • Must use with : --genetest
    		•
    --asum -au 0 No argument need
    Perform adaptive-sum gene-level analysis
  • Must use with : --genetest,--set/--setconsec
    		•
    --mfqls -qx 0 No argument need
    Perform MFQLS test.
    --mqlsconsec -qp NULL positive integer (>1)
    Perform MFQLS with given number of consecutive variants
  • Must use with : --mqls
    		•
    --mfhom -mo 0 No argument need
    Perform multi-FARVAT gene-level analysis under homogeneity assumption among phenotypes.
  • Can't use with : --mfhet,--longitudinal
  • Must use with : --genetest,--set/--setconsec
    		•
    --mfhet -mf 0 No argument need
    Perform multi-FARVAT gene-level analysis under heterogeneity assumption among phenotypes.
  • Can't use with : --hfhom,--longitudinal
  • Must use with : --genetest,--set/--setconsec
    		•
    --famvt -fv 0 No argument need
    Perform Variable Threshold gene-level test for family dataset.
  • Must use with : --genetest,--set/--setconsec
    		•
    --ggemma -zg NULL No argument need
    Perform gene-level GEMMA test.
  • Must use with : --genetest,--set/--setconsec
    		•
    --rvtdt -rd NULL No argument need
    Performs rv-TDT analysis, a TDT-based gene-level test for family data.
  • Can't use with :
  • Must use with :
    • --fbskat -fK NULL No argument need
    Performs FB-SKAT analysis, a SKAT-based gene-level test for family data.
  • Can't use with :
  • Must use with :
    • --lasso -la NULL No argument need
    Performs LASSO regression with gene-marker mapping file.
  • Can't use with :
  • Must use with :
    • --lassoall -lL NULL No argument need
    Performs LASSO regression and reports all variables in the set.
  • Can't use with :
  • Must use with :
    • --lassolambda -ll 0.1 Real value
    Cut lambda value for LASSO
  • Can't use with :
  • Must use with :

    • optcat_pway
    --pharaoh -gs 0 OT_ONOFF
    Perform PHARAOH analysis
  • Can't use with :
  • Must use with :
    • --progenesize -Pg NULL OT_RANGE
    Set the range of # variants in the gene to be included in the analysis
  • Can't use with :
  • Must use with :
    • --progsetsize -pt NULL OT_RANGE
    Set the range of # genes in the pathway to be included in the analysis
  • Can't use with :
  • Must use with :
    • --prolambda -Pl 1000 OT_STRING
    Set the fixed lambda penalty for PHARAOH
  • Can't use with :
  • Must use with :
    • --promaxiter -gq 100 OT_NUMBER
    Set the number of maximum iterations in PHARAOH
  • Can't use with :
  • Must use with :
    • --gesca -ge 0 OT_ONOFF
    Perform GeSCA
  • Can't use with :
  • Must use with :
    • --ggpath -gp NULL OT_STRING
    Gene-gene path data for pathway
  • Can't use with :
  • Must use with :
    • --gsetconsec -GC NULL OT_RANGE
    Automatically generates gene-set definition by consecutive manner
  • Can't use with :
  • Must use with :
    • --gxg -gg NULL No argument need
    Performs GxG interaction test in regression analysis. Note that only two-way interaction will be assessed.
  • Can't use with :
  • Must use with :
    • --gxgall -gX NULL OT_ONOFF
    Perform GxG analysis with all variables into a single model
  • Can't use with :
  • Must use with :
    • --gxglambda -xb NULL OT_STRING
    List of lambdas of gene/pathway to try for gene-gene interaction
  • Can't use with :
  • Must use with :
    • --gxglist -xl NULL OT_STRING
    List of gene pairs to test gene-gene interaction
  • Can't use with :
  • Must use with :

    • Single analysis related
    --scoretest -ct 0 No argument need
    Perform variant-level score test (both for Rao's score test and Generalizaed score test)
    --lrt -lr 0 No argument need
    Perform LRT test based on variant-wise model additional to the score test (it will takes much time)
  • Must use with : --scoretest
    		•
    --qls -ql 0 No argument need
    Perform quasi-likelihood scoretest analysis
    --fastfqls -FF 0 OT_ONOFF
    Perform fast version of FQLS with genotype imputation
  • Can't use with :
  • Must use with :
    • --fqls -qf 0 No argument need
    Perform quasi-likelihood scoretest analyiss using pedigree structure
    --fqlsnopddt -pf 0 No argument need
    When perform Family QLS, do not force to use kinship coefficient when computing the offset of each sample.
  • Must use with : --fqls,--mfqls
    		•
    --retestthr -rt 0.05 real number (0~1)
    Set the p-value threshold to perform second-level unimputed FQLS when after imputed FQLS. Lesser number of variants will be incorporated as lesser this value
  • Must use with : --fqls
    		•
    --fastmqls -Fa 0 OT_ONOFF
    Perform fast version of MQLS with genotype imputation
  • Can't use with :
  • Must use with :
    • --mqls -qm 0 No argument need
    Perform Modified QLStest. Note that MQLS will forcely disable genotype imputation when accompanied with --fqls so the analysis time will be long if there are missing genotypes
    --regression -rg 0 No argument need
    Perform variant-wise regression analysis. Linear or logistic regression will be selected according to phenotype
  • Can use with : --gxe,--avail,--sampvar,--pname,--cname,--pc2cov
    		•
    --donull -dn NULL No argument need
    When performing regression analysis with --regression, fit null model and export its results.
  • Must use with : --regression
    		•
    --fisher -fy NULL No argument need
    Perform variant-level Fisher's Exact test using final dataset.
    --trend -CA NULL No argument need
    Perform variant-level Cochran-Armitage trend test using final dataset.
    --gemma -G 0 No argument need
    Performs GEMMA
    --tdt -td NULL No argument need
    Perform Transmission Disequilibrium Test (TDT). Note that this test requires pedigree information.
    --sdt -st NULL No argument need
    Perform Sibship Disequilibrium Test (SDT). Note that this test requires pedigree information and multiple siblings for each family.

    Genetic summary related
    --lod -lo NULL No argument need
    Perform LoD analysis
    --fst -Ft NULL No argument need
    Compute Fst for each marker. Note that gene-wise Fst will be computed with --set.
    --ld -ld 0 No argument need
    Perform pair-wise LD computation with given conditions, exhaustive pair LD will be computed unless no further condition is assigned
    --ldcor -lc 0 No argument need
    Compute LD based on Pearson's correlation coefficient.
  • Must use with : --ld
    		•
    --ldvar -lM NULL Variant identifiers divided by comma(,) w/o whitespace or file path
    Determine the variant to investigate exhaustive two-way LD.
  • Must use with : --ld
    		•
    --ldbin -lb 0 No argument need
    Constraints LD computation to make pair for only N adjacent variants. Adjacency will be determined with chromosome and position
  • Can't use with : --ldsize
  • Must use with : --ld
    		•
    --ldcontrast -lx NULL OT_ONOFF
    Perform LD contrast method
  • Can't use with :
  • Must use with :
    • --ldsize -lS 0 Positive integer
    Constraints LD computation to make pair for the variants within specified range. Adjacency will be determined with chromosome and position
  • Can't use with : --ldbin
  • Must use with : --ld
    		•
    --density -de 0 No argument need
    Investigate the density of variants based on their physical positions on the chromosome and make a histogram-like report
    --tstv -tt 0 No argument need
    Investigate ts/tv ratio of the variants by the window that based on their physical positions on the chromosome and make a report for them
    --dsgdist -dd NULL No argument need
    Export dosage distribution
  • Must use with : --dosage
    		•
    --mendel -m NULL No argument need
    Perform the integrity of Mendel inheritance across families.
    --famuniq -fU NULL No argument need
    Export the list of variants having its minor allele only for specific family, not the other family.
    --popuniq -pU NULL No argument need
    Based on the population definition, reports the list of population-specific variants.
  • Can't use with :
  • Must use with :
    • --monotone -tm NULL No argument need
    Export the list of variants having no minor allele. Note that the definition of 'having no minor allele' might be depends on the dataset or filters applied.
    --singleton -ts NULL No argument need
    Export the list of variants having only one minor allele. Note that the definition of 'having no minor allele' might be depends on the dataset or filters applied.
    --doubleton -tb NULL No argument need
    Export the list of variants having only two minor allele. Note that the definition of 'having no minor allele' might be depends on the dataset or filters applied.
    --freq -f founder all / founder / corr
    Compute and export minor-allele frequency for each variant. Samples included to get MAF will vary on the parameter
    --hwe -H founder all / founder / corr(Not implemented)
    Compute and export the result of Hardy-Weinberg Equilibrium test. Samples included to perform test will vart on the parameter
    --miss -mx NULL No argument need
    Investigate genotype missingness against variant/sample/family and make report.
    --mistest -mt NULL No argument need
    Perform a test for genotype missingness is random or not.
  • Must use with : --miss
    		•
    --inbreed -ib NULL No argument need
    Compute sample-wise inbreeding coefficient F.
    --variantsummary -ks NULL No argument need
    Write out a comprehensive summary for variants, in a chromosome-wise manner.
    --hethom -hh NULL OT_ONOFF
    Compute sample-site het/hom ratio

    Miscellaneous
    --grm -gR NULL file path
    Read the sample relatedness matrix computed from GCTA, and perform statistical analysis with the sample relatedness matrix computed from WISARD
    --grmalpha -ga 0.001 real number(0~1)
    Set the alpha for confidence interval on the statistical analysis by --grm
  • Must use with : --grm
    		•
    --pca -P 0 No argument need
    Perform Principal Component Analysis (PCA)
  • Can use with : --npc,--proppc,--fullpca
    		•
    --npc -N 5 positive integer
    Determine the number of PCs computed. Note that this number cannot larger than the number of samples
  • Can't use with : --proppc,--fullpca
  • Must use with : --pca
    		•
    --proppc -pp NULL Real value ranged (0,1]
    Extract an arbitrary number of PCs to explain given proportion of entire variance.
  • Can't use with : --npc,--fullpca
  • Must use with : --pca
    		•
    --fullpca -fu 0 No argument need
    Perform full PCA with spectral decomposition. This option require much more time, but can compute all possible PCs
  • Can't use with : --npc,--proppc
  • Must use with : --pca
    		•
    --pc2cov -p2 NULL No argument need
    Incorporate computed PCs as covariates
  • Must use with : --pca
    		•
    --mds -MD NULL No argument need
    Generate MDS plot points and draw if possible
  • Can't use with :
  • Must use with :
    • --adjust -A NULL No argument need
    Apply multiple testing corretion method to the result, and produce extra result.
    --genoctrl -gl NULL No argument need
    Use genomic control method to adjust p-values when performing multiple testing correction.
  • Must use with : --adjust
    		•
    --usergc -eg NULL Positive real number
    When applying multiple testing correction to the analysis, assign user-defined Genomic control value instead of compute it from given statistics.
  • Must use with : --adjust
    		•
    --version -v NULL No argument need
    Print the version of WISARD and silently stop. No further analyses will be performed when this option is given.
    --citation -ce NULL No argument need
    Print out the information for citation of this program and exit.
    --quiet -q NULL No argument need
    Suppress all visible outputs of execution. Note that the log will be normally produced.
    --explore -e NULL No argument need
    Launch interactive shell for exploration of final dataset

    For debug
    --testmatrix -Xm 0 No argument need
    Perform the exhaustive testing for matrix-related problem.
    --testmatfunc -Xt 0 No argument need
    Perform the test for matrix functionality, not available in public version.
    --testmatclass -Xc 0 No argument need
    Perform the test for matrix class, not available in public version.
    --testfunc -Xf 0 No argument need
    Perform the test for functionality, not available in public version.
    --check -ck 0 No argument need
    Check system, not available in public version.
    --makenrm -my NULL No argument need
    Export normalized genotype information
    --group -g NULL file path
    Define a group for samples or variants 
    NOTDOCUM data
    EXCLREQU data
    NOPTTYPE data
    DETADESC data
    NOTDOCUM sampvarflag
    EXCLREQU sampvarflag
    NOPTTYPE sampvarflag
    DETADESC sampvarflag
    NOTDOCUM variantvar
    EXCLREQU corepacts
    NOPTTYPE corepacts
    DETADESC corepacts
    NOTDOCUM varwindow
    EXCLREQU varwindow
    NOPTTYPE varwindow
    DETADESC varwindow
    NOTDOCUM filmaf
    EXCLREQU filmaf
    NOPTTYPE filmaf
    DETADESC filmaf
    NOTDOCUM incmaf
    EXCLREQU incmaf
    NOPTTYPE incmaf
    DETADESC incmaf
    EXCLREQU makeflag
    NOPTTYPE makeflag
    DETADESC makeflag
    EXCLREQU sepid
    NOPTTYPE sepid
    DETADESC sepid
    NOTDOCUM outmisgeno
    EXCLREQU outmisgeno
    NOPTTYPE outmisgeno
    DETADESC outmisgeno
    EXCLREQU gsetconsec
    NOPTTYPE gsetconsec
    DETADESC gsetconsec
    EXCLREQU species
    EXCLREQU nodata
    EXCLREQU regex
    NOPTTYPE regex
    DETADESC regex
    NOTDOCUM model
    EXCLREQU model
    NOPTTYPE model
    DETADESC model
    EXCLREQU fastmqls
    NOPTTYPE fastmqls
    DETADESC fastmqls
    EXCLREQU fastfqls
    NOPTTYPE fastfqls
    DETADESC fastfqls
    NOTDOCUM genemiss
    EXCLREQU pedgene
    NOPTTYPE pedgene
    DETADESC pedgene
    NOTDOCUM adjf1
    EXCLREQU adjf1
    NOPTTYPE adjf1
    DETADESC adjf1
    NOTDOCUM adjf2
    EXCLREQU adjf2
    NOPTTYPE adjf2
    DETADESC adjf2
    NOTDOCUM makefarvat
    EXCLREQU makefarvat
    NOPTTYPE makefarvat
    DETADESC makefarvat
    EXCLREQU farvatx
    NOPTTYPE farvatx
    DETADESC farvatx
    EXCLREQU farvatxndiv
    NOPTTYPE farvatxndiv
    DETADESC farvatxndiv
    EXCLREQU farvatxd
    NOPTTYPE farvatxd
    DETADESC farvatxd
    NOTDOCUM hmdrall
    EXCLREQU hmdrall
    NOPTTYPE hmdrall
    DETADESC hmdrall
    EXCLREQU hmdrprior
    NOPTTYPE hmdrprior
    DETADESC hmdrprior
    EXCLREQU pharaoh
    NOPTTYPE pharaoh
    DETADESC pharaoh
    NOTDOCUM proopt
    EXCLREQU proopt
    NOPTTYPE proopt
    DETADESC proopt
    EXCLREQU prolambda
    NOPTTYPE prolambda
    DETADESC prolambda
    NOTDOCUM prorange
    EXCLREQU prorange
    NOPTTYPE prorange
    DETADESC prorange
    NOTDOCUM prothr
    EXCLREQU prothr
    NOPTTYPE prothr
    DETADESC prothr
    EXCLREQU promaxiter
    NOPTTYPE promaxiter
    DETADESC promaxiter
    EXCLREQU progenesize
    NOPTTYPE progenesize
    DETADESC progenesize
    EXCLREQU progsetsize
    NOPTTYPE progsetsize
    DETADESC progsetsize
    NOTDOCUM prosingle
    EXCLREQU prosingle
    NOPTTYPE prosingle
    DETADESC prosingle
    NOTDOCUM propermcov
    EXCLREQU propermcov
    NOPTTYPE propermcov
    DETADESC propermcov
    EXCLREQU seqperm
    NOPTTYPE seqperm
    DETADESC seqperm
    EXCLREQU permfile
    NOPTTYPE permfile
    DETADESC permfile
    EXCLREQU gesca
    NOPTTYPE gesca
    DETADESC gesca
    NOTDOCUM modeltype
    EXCLREQU modeltype
    NOPTTYPE modeltype
    DETADESC modeltype
    EXCLREQU ggpath
    NOPTTYPE ggpath
    DETADESC ggpath
    NOTDOCUM makecolgeno
    EXCLREQU makecolgeno
    NOPTTYPE makecolgeno
    DETADESC makecolgeno
    NOTDOCUM debug
    EXCLREQU debug
    NOPTTYPE debug
    DETADESC debug
    NOTDOCUM help
    EXCLREQU help
    NOPTTYPE help
    DETADESC help
    EXCLREQU expression
    NOPTTYPE expression
    DETADESC expression
    NOTDOCUM nsim
    EXCLREQU nsim
    NOPTTYPE nsim
    DETADESC nsim
    NOTDOCUM sim
    EXCLREQU sim
    NOPTTYPE sim
    DETADESC sim
    NOTDOCUM sigmaf
    EXCLREQU sigmaf
    NOPTTYPE sigmaf
    DETADESC sigmaf
    EXCLREQU makebcf
    EXCLREQU makemdr
    NOPTTYPE makemdr
    NOTDOCUM shuffle
    EXCLREQU shuffle
    NOPTTYPE shuffle
    DETADESC shuffle
    NOTDOCUM annovar
    NOPTTYPE annovar
    DETADESC annovar
    DETADESC lod
    EXCLREQU popuniq
    NOPTTYPE setoverlap
    DETADESC setoverlap
    EXCLREQU setrandom
    NOPTTYPE setrandom
    DETADESC setrandom
    EXCLREQU napheno
    NOPTTYPE napheno
    DETADESC napheno
    NOTDOCUM emmax
    EXCLREQU emmax
    DETADESC emmax
    EXCLREQU mds
    DETADESC mds
    EXCLREQU gxg
    NOTDOCUM forceconv
    EXCLREQU forceconv
    NOPTTYPE forceconv
    DETADESC forceconv
    NOTDOCUM dfam
    EXCLREQU dfam
    NOPTTYPE dfam
    NOTDOCUM updallele
    EXCLREQU updallele
    DETADESC updallele
    NOTDOCUM window
    DETADESC window
    NOTDOCUM ci
    EXCLREQU ci
    DETADESC ci
    EXCLREQU lasso
    EXCLREQU lassolambda
    DETADESC lassolambda
    EXCLREQU lassoall
    NOTDOCUM pls
    EXCLREQU pls
    NOPTTYPE pls
    DETADESC pls
    NOTDOCUM sampleweight
    EXCLREQU sampleweight
    DETADESC sampleweight
    EXCLREQU rvtdt
    EXCLREQU fbskat
    EXCLREQU nskip
    EXCLREQU singleparent
    NOPTTYPE singleparent
    DETADESC singleparent
    DETADESC bcf
    DETADESC mdrthr
    EXCLREQU ldcontrast
    NOPTTYPE ldcontrast
    DETADESC ldcontrast
    NOTDOCUM flip
    EXCLREQU flip
    NOPTTYPE flip
    DETADESC flip
    NOTDOCUM varsubset
    EXCLREQU varsubset
    NOPTTYPE varsubset
    DETADESC varsubset
    NOPTTYPE hethom
    DETADESC hethom
    NOTDOCUM markercheck
    EXCLREQU markercheck
    NOPTTYPE markercheck
    DETADESC markercheck
    NOTDOCUM meta
    EXCLREQU meta
    NOPTTYPE meta
    DETADESC meta
    NOTDOCUM fid
    EXCLREQU fid
    NOPTTYPE fid
    DETADESC fid
    NOTDOCUM outformat
    EXCLREQU outformat
    NOPTTYPE outformat
    DETADESC outformat
    EXCLREQU maf
    DETADESC maf
    NOTDOCUM het
    EXCLREQU het
    NOPTTYPE het
    DETADESC het
    NOTDOCUM variantblup
    EXCLREQU variantblup
    NOPTTYPE variantblup
    DETADESC variantblup
    EXCLREQU famsplit
    NOPTTYPE famsplit
    DETADESC famsplit
    EXCLREQU setspan
    NOPTTYPE setspan
    DETADESC setspan
    NOTDOCUM tridge
    EXCLREQU tridge
    NOPTTYPE tridge
    DETADESC tridge
    EXCLREQU hamming
    NOPTTYPE hamming
    DETADESC hamming
    NOTDOCUM baldingnichols
    EXCLREQU baldingnichols
    NOPTTYPE baldingnichols
    DETADESC baldingnichols
    EXCLREQU fuzzymdr
    NOPTTYPE fuzzymdr
    DETADESC fuzzymdr
    EXCLREQU gxgall
    NOPTTYPE gxgall
    DETADESC gxgall
    EXCLREQU gxglist
    NOPTTYPE gxglist
    DETADESC gxglist
    EXCLREQU gxglambda
    NOPTTYPE gxglambda
    DETADESC gxglambda
    NOTDOCUM prunevif
    EXCLREQU prunevif
    NOPTTYPE prunevif
    DETADESC prunevif
    NOTDOCUM prunepw
    EXCLREQU prunepw
    NOPTTYPE prunepw
    DETADESC prunepw
    NOTDOCUM selgene
    EXCLREQU selgene
    NOPTTYPE selgene
    DETADESC selgene
    NOTDOCUM remgene
    EXCLREQU remgene
    NOPTTYPE remgene
    DETADESC remgene
    NOTDOCUM ption
    DETADESC ption
    NOTDOCUM lassolabmda
    EXCLREQU lassolabmda


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    Last modified : 2017-07-22 22:28:44

    Prof. Won's labratory and Bioinformatics and Biostatistics (BIBS) labratory, Seoul National University.

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