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Per-allele filters?

I'm doing analysis on a large multi-ancestry project (XX,XXX exomes) in which approximately 20% of variant sites are multi-allelic. Our sequencing/calling is done at the Broad. It seems that at these multi-allelic sites, only one filter is applied. For example, where there is a SNP and an indel, the SNP may get an indel filter.

Is it possible to disclose how the filter at a given site is chosen? (E.g., by severity, etc.) Is there a plan to allow each variant to have its own filter in the future? (Not sure if there is an internal Broad place to discuss this, since it may have to do more with the pipeline and how SNPs and indel calls are combined than the GATK per se.)

Answers

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