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better docs for Qualify Missing Intervals 

now that it's available to the public, better give'em good docs!
This commit is contained in:
Mauricio Carneiro 2013-06-10 15:17:40 -04:00
parent c84f0deb1d
commit 1d67d07cf1
1 changed files with 2 additions and 1 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
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@ -87,7 +87,7 @@ import java.util.List;
* *
* <h3>Input</h3> * <h3>Input</h3>
* <p> * <p>
* A reference file * A reference file (for GC content), the input bam file (for base and mapping quality calculation), the missing intervals (in the -L), the baits/targets used to sequence (in the -targets) and a bed file with the coding sequence intervals of the genome (in the -cds)
* </p> * </p>
* *
* <h3>Output</h3> * <h3>Output</h3>
@ -100,6 +100,7 @@ import java.util.List;
* java -Xmx2g -jar GenomeAnalysisTK.jar \ * java -Xmx2g -jar GenomeAnalysisTK.jar \
* -T QualifyMissingIntervals \ * -T QualifyMissingIntervals \
* -R ref.fasta \ * -R ref.fasta \
* -I input.bam \
* -o output.grp \ * -o output.grp \
* -L input.intervals \ * -L input.intervals \
* -cds cds.intervals \ * -cds cds.intervals \