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Matching bam file with GATK BQSR report
Buys de Barbanson edited this page Feb 25, 2020
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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.