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broadinstitute / gatk-protected

Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead
BSD 3-Clause "New" or "Revised" License
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Downsample ref reads in Mutect #1111

Closed davidbenjamin closed 7 years ago

davidbenjamin commented 7 years ago

We could save a lot of time in PairHMM if we could identify reads supporting the reference allele and run PairHMM only on reads supporting alt alleles and a random sample of ref reads. This could especially save a lot of time on deep, low-AF sequencing, such as cfDNA. One simple criterion for ref-ness that might work would be whether a read gets threaded onto the reference path in the assembly graph.

droazen commented 7 years ago

Issue moved to broadinstitute/gatk #3021 via ZenHub