From 22bf0528280630b1ae16e04a465d85a0b6e2922d Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 1 Aug 2012 13:17:16 -0400 Subject: [PATCH] Fixing BQSR GATK docs --- .../sting/gatk/walkers/bqsr/BaseRecalibrator.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 b2400a49d..06f42cbad 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 @@ -58,7 +58,7 @@ import java.util.ArrayList; * This walker is designed to work as the first pass in a two-pass processing step. It does a by-locus traversal operating * only at sites that are not in dbSNP. We assume that all reference mismatches we see are therefore errors and indicative * of poor base quality. This walker generates tables based on various user-specified covariates (such as read group, - * reported quality score, cycle, and dinucleotide). Since there is a large amount of data one can then calculate an empirical + * reported quality score, cycle, and context). Since there is a large amount of data one can then calculate an empirical * probability of error given the particular covariates seen at this site, where p(error) = num mismatches / num observations. * The output file is a table (of the several covariate values, num observations, num mismatches, empirical quality score). *

@@ -90,7 +90,7 @@ import java.util.ArrayList; *

Examples

* 
  * java -Xmx4g -jar GenomeAnalysisTK.jar \
- *   -T BaseQualityScoreRecalibrator \
+ *   -T BaseRecalibrator \
  *   -I my_reads.bam \
  *   -R resources/Homo_sapiens_assembly18.fasta \
  *   -knownSites bundle/hg18/dbsnp_132.hg18.vcf \