Hwo to identify that BQSR is performed on CRAM file
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12 months ago
Sd • 0

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 • 774 views
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12 months ago
raphael.B ▴ 520

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

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