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Detail of [all.hwe]

A computed HWE using all samples

Output format is TSV

Column	Format	Modifier	Description
CHR	Positive integer	NONE	The rank of least conditional variance
VARIANT	Positive integer	NONE	The rank of least conditional variance
POS	Positive integer	NONE	The rank of least conditional variance
ALT	Positive integer	NONE	The rank of least conditional variance
ANNOT	Positive integer	NONE	The rank of least conditional variance
GENO	integer/integer/integer	NONE	Number of alleles for each of aa/Aa/AA, respectively
O(HET)	integer	NONE	Observed number of heterozygotes
E(HET)	real	NONE	Expected number of heterozygotes
STAT_HWE	real	NONE	Statistic of Hardy-Weinberg Equilibrium test
P_HWE	real	NONE	Exact p-value of HWE test
NIND	integer	NONE	Incorporated number of individuals for the test

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 F_ST 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