java -jar GenomeAnalysisTK.jar -T AnalyzeCovariates -R myrefernce.fasta -BQSR myrecal.table -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 |