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Does trimming affect the variant calling?

JulsJuls Member ✭✭
edited December 2019 in Ask the GATK team

Dear GATK team,

I am aware that you do not particularly recommend adapter or quality trimming, as discussed here:
https://gatkforums.broadinstitute.org/gatk/discussion/2957/read-trimming

However, does it negatively affect it? I am using a bunch of tools on the same bam files - some benefit from adapter trimming. Is it ok to feed the same trimmed bam files (trimmed with trimmomatic as recommended in the manual for DNAseq) into GATK variant calling pipeline (HC or Mutect2) or will there be any negative consequences?

Thanks for you help!

Best Answers

  • davidbendavidben Boston ✭✭✭
    Accepted Answer

    @Juls those base quality thresholds (3, 3, and 15 if I understand correctly) are quite conservative. I would not worry about them harming the performance of GATK tools.

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