From 8c18ead5e42aaebb9dd6bd9cd2a97be8c3de5567 Mon Sep 17 00:00:00 2001 From: Laura Gauthier Date: Mon, 20 Jul 2015 13:22:40 -0400 Subject: [PATCH] Clarify VCF version for supporting population alleles files Clarify DeNovoPrior definition on PbyT --- .../gatk/tools/walkers/phasing/PhaseByTransmission.java | 4 +++- .../walkers/variantutils/CalculateGenotypePosteriors.java | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java index 709711064..4ff278755 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java @@ -118,7 +118,9 @@ import java.util.*; * remain in mendelian violation after being assigned the most likely genotype combination will be reported * there. Information reported: chromosome, position, filter, allele count in VCF, family, transmission * probability, and each individual genotype, depth, allelic depth and likelihoods. - *
  • DeNovoPrior: Mutation prio; default is 1e-8
    • + *
  • DeNovoPrior: Prior probability of de novo mutations. The default value of 1e-8 is fairly stringent, so if + * you are interested in maximizing sensitivity at the expense of specificity (i.e. are ok with seeing some false + * positives as long as all true positives are detected) you will need to relax this value.
    • * * *

    Output

    diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java index 15b0ed0e8..9d92a4b8a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java @@ -196,7 +196,7 @@ public class CalculateGenotypePosteriors extends RodWalker { /** * Supporting external panels. Allele counts from these panels (taken from AC,AN or MLEAC,AN or raw genotypes) will - * be used to inform the frequency distribution underying the genotype priors. + * be used to inform the frequency distribution underying the genotype priors. These files must be VCF 4.2 spec or later. */ @Input(fullName="supporting", shortName = "supporting", doc="Other callsets to use in generating genotype posteriors", required=false) public List> supportVariants = new ArrayList<>();