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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2012-08-01 13:17:36 -04:00
parent 9ac72dbd4d 22bf052828
commit 52b93cab62
1 changed files with 2 additions and 2 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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@ -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).
* <p>
@ -94,7 +94,7 @@ import java.util.ArrayList;
* <h2>Examples</h2>
* <pre>
* 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 \