Dear GATK Team,
I understand that with many GATK tools, default Read filters are applied. However, these differ between tools and therefore, differ between steps of Best Practices Workflows, such as between Mutect2 and GetPileupSummaries as part of the Somatic short variant discovery (SNVs + Indels).
When using tools in one workflow, such as the Somatic short variant discovery (SNVs + Indels), why are read filters not all applied from the outset or kept the same throughout the workflow?
Thank you for your time and help.
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