Matching bam file with GATK BQSR report

When recalibrating a bam file with many cells, maybe even from different sequencing runs the GATK recalibration report is sometimes missing covariates for some read groups. This is not a big deal, those read groups usually have very few reads and are discarded by the BaseRecalibrator tool. The ApplyBQSR will however crash when applying recalibration to the bam file.

Use: bamMatchGATKBQSRReport.py original.bam bqsr_report.tsv cleaned.bam to obtain a bam file cleaned.bam which does not contain the read groups for which no covariates are available.