Category

Genome Variant Analysis


Usage

java -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R reference.fasta -V input.vcf -o output.withPosteriors.vcf --ignoreInputSamples


Manual

Argument name(s)Default valueSummary
Required Inputs
--variant
 -V
NAInput VCF file
Optional Inputs
--supporting
[]Other callsets to use in generating genotype posteriors
Optional Outputs
--out
 -o
stdoutFile to which variants should be written
Optional Parameters
--deNovoPrior
 -DNP
1.0E-6The de novo mutation prior
--globalPrior
 -G
0.001The global Dirichlet prior parameters for the allele frequency
--numRefSamplesIfNoCall
 -nrs
0The number of homozygous reference to infer were seen at a position where an "other callset" contains no site or genotype information
Optional Flags
--defaultToAC
 -useAC
falseUse the AC field as opposed to MLEAC. Does nothing if VCF lacks MLEAC field
--discoveredACpriorsOff
 -useACoff
falseDo not use discovered allele count in the input callset for variants that do not appear in the external callset.
--ignoreInputSamples
 -ext
falseUse external information only; do not inform genotype priors by the discovered allele frequency in the callset whose posteriors are being calculated. Useful for callsets containing related individuals.
--skipFamilyPriors
 -skipFam
falseSkip application of family-based priors
--skipPopulationPriors
 -skipPop
falseSkip application of population-based priors


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