From 5a875cb841c0426aa0b8811db2a5a55fff270fca Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Thu, 13 Aug 2015 16:40:42 -0400 Subject: [PATCH] Fixed missing code tag --- .../walkers/variantutils/CalculateGenotypePosteriors.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) 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 884193184..dc9b06354 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 @@ -81,7 +81,7 @@ import java.util.*; * *

* Given a VCF with genotype likelihoods from the HaplotypeCaller, UnifiedGenotyper, or another source which provides - * -unbiased- genotype likelihoods, calculate the posterior genotype state and likelihood given allele frequency + * unbiased genotype likelihoods, calculate the posterior genotype state and likelihood given allele frequency * information from both the samples themselves and input VCFs describing allele frequencies in related populations.

* *

The AF field will not be used in this calculation as it does not provide a way to estimate the confidence interval @@ -139,7 +139,8 @@ import java.util.*; * -R reference.fasta \ * -V NA12878.wgs.HC.vcf \ * -supporting 1000G_EUR.genotypes.combined.vcf \ - * -o NA12878.wgs.HC.posteriors.vcf \ + * -o NA12878.wgs.HC.posteriors.vcf + * * *

Refine the genotypes of a large panel based on the discovered allele frequency

*