java -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R reference.fasta -V input.vcf -o output.withPosteriors.vcf
Argument name(s) | Default value | Summary | |
---|---|---|---|
Required Inputs | |||
--variant  -V | NA | Input VCF file | |
Optional Inputs | |||
--supporting | [] | Other callsets to use in generating genotype posteriors | |
Optional Outputs | |||
--out  -o | stdout | File to which variants should be written | |
Optional Parameters | |||
--deNovoPrior  -DNP | 1.0E-6 | The de novo mutation prior | |
--globalPrior  -G | 0.001 | The global Dirichlet prior parameters for the allele frequency | |
--numRefSamplesIfNoCall  -nrs | 0 | The number of homozygous reference to infer were seen at a position where an "other callset" contains no site or genotype information | |
Optional Flags | |||
--defaultToAC Â -useAC | false | Use the AC field as opposed to MLEAC. Does nothing if VCF lacks MLEAC field | |
--discoveredACpriorsOff  -useACoff | false | Do not use discovered allele count in the input callset for variants that do not appear in the external callset. | |
--ignoreInputSamples  -ext | false | Use 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 | false | Skip application of family-based priors | |
--skipPopulationPriors  -skipPop | false | Skip application of population-based priors |