The frontline support team will be slow on the forum because we are occupied with a GATK Workshop on March 26th and 27th 2019. We will be back and available to answer questions on the forum on March 28th 2019.
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?