Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Doesn't Base Quality Score Recalibration degrade sensitivity in heavily mutated cancers?
From the GATK FAQs - "The base quality score recalibrator treats every reference mismatch as indicative of machine error"... which is why we have to give it a list of dbSNPs to skip over. But what about somatic SNPs? Wouldn't hypermutated tumors from uterine, colorectal, melanoma, or lung cancers be re-calibrated to a lower quality than data from AML or breast. And variant caller sensitivity would drop accordingly.
Should we ideally do some high-confidence SNP calling on un-calibrated BAMs, and append those to the dbSNP VCF for the BQSR?