java -jar GenomeAnalysisTK.jar -T AnalyzeCovariates -R myrefernce.fasta -ignoreLMT -BQSR recal1.table \ # you can discard any two -before recal2.table -after recal3.table -plots myrecals.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 |