java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R reference.fasta -I myinput.bam -knownSites bundle/my-trusted-snps.vcf \ # optional but recommended -knownSites bundle/my-trusted-indels.vcf \ # optional but recommended -o firstpass.table # Generate the second pass recalibration table file java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R reference.fasta -I myinput.bam -knownSites bundle/my-trusted-snps.vcf -knownSites bundle/my-trusted-indels.vcf -BQSR firstpass.table -o secondpass.table # Finally generate the plots and also keep a copy of the csv (optional) java -jar GenomeAnalysisTK.jar -T AnalyzeCovariates -R reference.fasta -before firstpass.table -after secondpass.table -csv BQSR.csv \ # optional -plots BQSR.pdf
| Set | Argument | Label | Color | Description |
|---|---|---|---|---|
| Original | -before | BEFORE | Pink | First pass recalibration tables obtained from applying BaseRecalibration on the original alignment. |
| Recalibrated | -after | AFTER | Blue | Second pass recalibration tables results from the application of BaseRecalibration on the alignment recalibrated using the first pass tables |
| Input | -BQSR | BQSR | Black | Any recalibration table without a specific role |