WISARD[wɪzərd]
Workbench for Integrated Superfast Association study with Related Data
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Output Index

Here is the list of all outputs produced from WISARD.
Suffix Format Produced by Affected by Description
log arbitrary NONE --verbose A complete log file produced from an execution of WISARD
gene.res TSV --genetest --skat
--skato
--pedcmc
A result of gene-level test (Burden, SKAT, SKAT-o, PEDCMC)
simple.qls.res TSV --qls NONE A result of QLS analysis
extended.qls.res TSV --mfqls --mqlsconsec A result of Extended QLS analysis
all.hwe TSV --hwe all NONE A computed HWE using all samples
founders.hwe TSV --hwe founder NONE A computed HWE using only founder samples
sampvar.res TSV --sxa NONE A result of computation of conditional variance for each sample
top.sampvar.res TSV --sxa --nsamp An ascending-sorted result of conditional variances
AI.blup TSV --makeblup --nostop
--emcount
--aithr
An estimation of BLUP using EM-AI algorithm for REML model
NR.blup TSV --makeblup
--ml
--nostop
--emcount
An estimation of BLUP using Newton-Raphson algorithm for ML model
SD.blup TSV --makeblup
--specdcmp
NONE An estimation of BLUP using spectral decomposition
trend.res TSV --trend NONE A result of Cochran-Armitage trend test and allelic based test for the testing of association in case/control dataset
fisher.res TSV --fisher NONE A result of Fisher's exact test for the testing of association in case/control dataset
summary.variant.res TSV --variantsummary NONE A chromosome-wise summary for the various information from variants
tstv.variant.lst TSV --tstv NONE A result of Ts/Tv ratio by window
tstv.chr.lst TSV --tstv NONE A result of Ts/Tv ratio by chromosome
mistest.res TSV --mistest
binary phenotype
NONE A result of test of random missingness between case/control
inbreed.coef.res TSV --inbreed NONE A result of computation of inbreeding coefficient F
lod.res TSV --lod NONE A result of Log of Odds analysis
mendel.sample.res TSV --mendel NONE A result of analysis of sample-wise Mendelian transmission error
mendel.variant.res TSV --mendel NONE A result of analysis of variant-wise Mendelian transmission error
mendel.family.res TSV --mendel NONE A result of analysis of family-wise Mendelian transmission error
sample.miss.lst TSV --miss NONE A report of genotype missingness per sample
variant.miss.lst TSV --miss NONE A report of genotype missingness per variant
family.miss.lst TSV --miss NONE A report of genotype missingness per family
tdt.res TSV --tdt NONE A result of Transmission Disequilibrium Test
sdt.res TSV --sdt NONE A result of Sibship Disequilibrium Test
fst.res TSV --fst --set A result of FST estimation
variant.popuniq.res TSV --popuniq NONE A list of population-specific variants
variant.famuniq.res TSV --famuniq NONE A list of family-specific variants
variant.singleton.res TSV --singleton NONE A list of singleton variants (it means, there is only 'one' sample who having variant allele in a variant across final dataset)
variant.monotone.res TSV --monotone NONE A list of monotone variants (it means, there is no sample who having variant allele in a variant across final dataset)
variant.doubleton.res TSV --doubleton NONE A list of doubleton variants (it means, there is only 'two' sample who having variant allele in a variant across final dataset)
gene.fail.lst LIST --genetest --skato A list of gene names that failed to perform SKAT-o test
filter.sample.lst TSV --incgeno
--filgeno
NONE A list of sample filtering status by filtering criteria
allmiss.sample.lst TSV NONE NONE A list of samples having NO available genotype
linear.regr.res TSV --regression --interaction A result of regression analysis with continuous phenotype
logistic.regr.res TSV --regression --interaction A result of regression analysis with dichotomous phenotype
family.qls.res TSV --fqls --mqls
--avail
--fqlsnopddt
--retestthr
A result of Family QLS analysis
estimated.maf TSV --freq corr NONE An estimated MAF from sample relatedness
all.maf TSV --freq all NONE A computed MAF using all samples
founders.maf TSV --freq founder NONE A computed MAF using only founder samples
power.single.res TSV --powercalc NONE A result of power calculation from single phenotype
power.multi.res TSV --powercalc NONE A result of power calculation from multiple phenotypes
miss.pheno.lst TSV NONE --sampvar
--pname
A list of samples having phenotype missingness
miss.sex.lst TSV NONE NONE A list of samples having sex missingness
summary.gene.lst TSV --genetest
--genesummary
NONE A summary of analyzed gene-variant information
summary.gmap.lst TSV --genetest
--gmapsummary
Single binary phenotype
NONE A summary of variant distribution across case-control samples for each gene mapping
entire.dist.dsg TSV --dsgdist NONE A distribution of dosage for entire dataset
sample.dist.dsg TSV --dsgdist NONE A sample-wise distribution of dosage
ibs.cor matrix/TSV --ibs --cormat A matrix/list of pairs that contains computed IBS
empi.cor matrix/TSV --makecor --cormat A matrix/list of pairs that contains computed empirical kinship coefficients
empi.med.cor matrix/TSV --makecor
--medcor
--cormat A matrix/list of pairs that contains computed median of empirical kinship coefficients
theo.cor matrix/TSV --pddt --cormat A matrix/list of pairs that contains computed theoretical kinship coefficients based on the pedigree structure
hybrid.cor matrix/TSV --hybrid --cormat A matrix/list of pairs that contains mixed kinship coefficients
pearson.cor matrix/TSV --corpearson --cormat A matrix/list of pairs that contains Pearson's correlation coefficients
ktau.cor matrix/TSV --ktau --cormat A matrix/list of pairs that contains Kendall's tau correlation coefficients from raw genotype data
empi.ktau.cor matrix/TSV --empiktau --cormat A matrix/list of pairs that contains Kendall's tau correlation coefficients from normalized genotype data
ped PLINK PED --makeped NONE PED-formatted output of filtered dataset
map PLINK MAP --makeped
--makelgen
NONE MAP-formatted output of filtered dataset, accompanied by ped(--makeped) or lgen(--makelgen)
tped PLINK transposed PED --maketped NONE Transposed PED-formatted output of filtered dataset
tfam PLINK FAM --maketped NONE FAM-formatted output of filtered dataset, accompanied by tped
lgen Long-format dataset --makelgen NONE Long-formatted output of filtered dataset
vcf VCF --makevcf NONE VCF output of filtered dataset
bed PLINK binary PED --makebed NONE BED-formatted output of filtered dataset
bim PLINK FAM --makebed NONE BIM-formatted output of filtered dataset, accompanied by bed
fam PLINK FAM --makevcf
--makebed
--makelgen
NONE FAM-formatted output of filtered dataset, accompanied by bed(--makebed) or lgen(--makelgen)
raw PLINK RAW --makeraw
--makedom
--makerec
NONE RAW-formatted output of filtered dataset, additive-coded genotype
structure.fam ARBITRARY --famsummary NONE A report of retrieved pedigree structure
structure.nucl.fam ARBITRARY --ncsummary NONE A report of retrieved pedigree structure by nuclear family
qtest.res TSV --qtest NONE A result of Q-test
gemma.res TSV --femma NONE A result of GEMMA
mdr.res TSV --mdr NONE A result of MDR
pca.res TSV --pca --npc A list of computed PC scores
density.variant.lst TSV --density NONE A result of physical variant density by window
scoretest.res TSV --scoretest --lrt
--pddt
A result of Score test
covar.mat TSV --makecov --sampvar
--cname
--baseline
A matrix of covariates that actually used in the analyses, constructed from given covariates and final dataset
pheno.mat TSV --makepheno --sampvar
--pname
A matrix of phenotype(s) that actually used in the analyses, constructed from given phenotypes and final dataset
poly.est.res table --heritability --ml
--specdcmp
--aithr
A result of heritability estimation
altcor.miss.lst LIST --cor NONE A list of sample IDs consists of the samples not included in the final dataset, but exists in the alternative correlation file
samplist.miss.lst LIST --remsamp/--selsamp NONE A list of sample IDs consists of the samples not included in the final dataset, but exists in the sample list file
stat.sample.lst TSV NONE NONE A report of samples about whether sample is included in the final dataset or not, and the reason of the sample was not included if it was not included
gen GEN --makegen NONE GEN-formatted output of filtered dataset
sample SAMPLE --makegen/--makebgen NONE Sample information of GEN-formatted output
bgen Binary GEN --makebgen NONE Binarized GEN-formatted output of filtered dataset
variant.lst TSV --listvariant NONE A list of variant IDs that actually included in the final dataset
sample.lst TSV --listsample NONE A list of sample IDs that actually included in the final dataset
founder.lst TSV --listfounder NONE A list of founder sample IDs that actually included in the final dataset
allelic.excl.lst LIST --vcf NONE A list of variant IDs of the variants excluded before an analysis due to it contains more than two alleles (triallelic or polyallelic)
set.gene.lst LIST --makeset --settype Gene-marker definition formatted set after mapping between original gene-marker definition and final dataset


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Last modified : 2022-09-08 17:16:37