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Hwo to identify that BQSR is performed on CRAM file

Hi, I have a bunch of CRAM files of WGS that I want to check if Base Quality Score Recalibration (BQSR) has been done or not. Does anyone can help me how can I check it?

illumina gatk wgs sequencing bqsr
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updated by raphael.B • raphael.B • written by Sd • Sd

1 answer

If you run samtools view -H on your alignment file, you should have an entry starting with @PG ID:GATK ApplyBQSR .... in your CRAM/BAM header.

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written by raphael.B • raphael.B

Do you have an idea that how long on average does it take to run gatk ApplyBQSR on a whole genome sequencing (WGS) data? Does it necessary to perform this step on CRAMs?

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written by Sd • Sd

I don't know what are your computing resources but compared to the alignement itself it's quite short.

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written by raphael.B • raphael.B

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