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Hi GATK team,
I was wondering, your best practices for data preprocessing (https://software.broadinstitute.org/gatk/best-practices/workflow?id=11165) don't mention any trimming (using i.e. trim_galore or fastx). It seems like at least some time ago this was pretty standard. Does this mean it is not advised anymore? Can I really take my raw fastq file and map them using BWA directly, without any filtering?