From fabca66d09ca1ed9e15bc96628e5662db2188ad6 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Wed, 1 Aug 2012 14:52:49 -0400 Subject: [PATCH] Another fix to VQSR docs --- .../gatk/walkers/variantrecalibration/VariantRecalibrator.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index a2909d4ca..5e2125fb2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -63,7 +63,7 @@ import java.util.*; * The purpose of the variant recalibrator is to assign a well-calibrated probability to each variant call in a call set. * One can then create highly accurate call sets by filtering based on this single estimate for the accuracy of each call. * The approach taken by variant quality score recalibration is to develop a continuous, covarying estimate of the relationship - * between SNP call annotations (QD, SB, HaplotypeScore, HRun, for example) and the the probability that a SNP is a true genetic + * between SNP call annotations (QD, MQ, HaplotypeScore, and ReadPosRankSum, for example) and the the probability that a SNP is a true genetic * variant versus a sequencing or data processing artifact. This model is determined adaptively based on "true sites" provided * as input, typically HapMap 3 sites and those sites found to be polymorphic on the Omni 2.5M SNP chip array. This adaptive * error model can then be applied to both known and novel variation discovered in the call set of interest to evaluate the