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Does trimming affect the variant calling?
Dear GATK team,
I am aware that you do not particularly recommend adapter or quality trimming, as discussed here:
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!