From 740520c23beba300c7894321e5391a9d0420dbba Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 24 Aug 2012 13:20:10 -0400 Subject: [PATCH] Fix BQSR docs --- .../sting/gatk/walkers/bqsr/BaseRecalibrator.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index e45cad971..ea9d0976a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -56,7 +56,7 @@ import java.lang.reflect.Constructor; import java.util.ArrayList; /** - * First pass of the base quality score recalibration -- Generates recalibration table based on various user-specified covariates (such as reported quality score, cycle, and dinucleotide). + * First pass of the base quality score recalibration -- Generates recalibration table based on various user-specified covariates (such as read group, reported quality score, machine cycle, and nucleotide context). * *

* This walker is designed to work as the first pass in a two-pass processing step. It does a by-locus traversal operating