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 ddd75e232..512434e6d 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 @@ -62,7 +62,7 @@ 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). *
@@ -94,7 +94,7 @@ import java.util.ArrayList; *
* 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 \