Genome Variant Analysis


java -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R reference.fasta -supporting external.panel.vcf -V input.vcf -o output.withPosteriors.vcf --numRefSamplesIfNoCall 100


Argument name(s)Default valueSummary
Required Inputs
NAInput VCF file
Optional Inputs
[]Other callsets to use in generating genotype posteriors
Optional Outputs
stdoutFile to which variants should be written
Optional Parameters
1.0E-6The de novo mutation prior
0.001The global Dirichlet prior parameters for the allele frequency
0The number of homozygous reference to infer were seen at a position where an "other callset" contains no site or genotype information
Optional Flags
falseUse the AC field as opposed to MLEAC. Does nothing if VCF lacks MLEAC field
falseDo not use discovered allele count in the input callset for variants that do not appear in the external callset.
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.
falseSkip application of family-based priors
falseSkip application of population-based priors

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