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BQSR - perform on whole genome or single chromosomes OK?

astrandastrand New YorkMember


I am running GATK Best Practices again and just wanted to assure myself that I am proceeding correctly. I remember reading somewhere on here that BQSR performs best when given the whole genome to work with (similar to VQSR in that respect). Better to just run using the whole genome rather than giving it single chromosomes. I couldn't really find this comment/recommendation when I tried to look for it again, so wanted to see what the final word was on this. How should one proceed?


Best Answers


  • astrandastrand New YorkMember

    OK, thanks for the information.

  • astrandastrand New YorkMember

    To clarify, how exactly do I run BaseRecalibrator across multiple BAM files? As stated above, I would like to run it on whole genomes of individuals, so minimally, I would like to use as input all BAMs corresponding to each chromosome for a given individual. So can I just give it a file with the desired bam file names?

    I also have a related question: would it actually matter if I gave it all BAMs for all individuals in my dataset as opposed to just running on single individuals at a time?

    And there was a typo in your answer: I think you meant to say "BQSR will perform better on whole genomes, but you can probably get away with running on whole chromosomes."


  • astrandastrand New YorkMember

    Thanks, that answers all my questions.

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