To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

Effect of running BQSR per sample and not lane

jmhjmh EdinburghMember

What is the effect of running BQSR per sample across lanes and not per sample per lane i.e if @RG ID is per sample and not per sample lane. Does it introduce additional errors or just run BQSR sub-optimally? If So, how so?
Many Thanks

Best Answers

Answers

  • jmhjmh EdinburghMember

    Thanks for this, I have a follow up question. Are variants generated to boostrap the BQSR still valid if MarkDuplicates was run per combined sample? As I understand it MarkDups and IndelRealignment don't use RGID but work per Library and all the data. So If I ran GATK In the following manner:

    1. Align reads.
    2. Combine bams and markduplicates with picard
    3. Perform Indel realignment
    4. Initial run of haplotypecaller for bootstrap variants

    Then I can subsequently run BQSR using these variants as RGID wasn't used in these steps on reconstituted BAMs with read RGID correctly reflecting sample per lane. This means I don't have to run Haplotypecaller twice.
    Thanks for the help.

Sign In or Register to comment.