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Need to include custom interval list in gatk/processing-for-variant-discovery-gatk4
Not sure if this is a GATK question or Firecloud question, but:
According to this article, it is recommended that a set of intervals be used with BQSR when working with exomes. However, in the best practices pipelines that is posted on firecloud here made by @bshifaw does not include any clear way to directly use a more targeted interval list, and appears to actually just scatter over chromosomes (and this pipeline explicitly mentions that it can be used with WES data). In theory I'm fine with this but I wanted to ask - how important is it to use a set of intervals with BQSR for WES data? Is it ok to leave this as is, or should I include an interval list?