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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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Filter reads more aggressively in Mutect #1110

Closed davidbenjamin closed 7 years ago

davidbenjamin commented 7 years ago

The traditional approach in Mutect and HaplotypeCaller is to filter reads based on simple properties, such as low mapping quality, lack of mate, etc. This still leaves a lot of fairly bad reads. These probably don't affect calls because they don't support any allele well according to PairHMM. Still, they probably waste a lot of time by generating unnecessary paths in the assembly graph.

Some possible filters include an excessive number of different CIGAR elements, and too many low-quality bases.

droazen commented 7 years ago

Issue moved to broadinstitute/gatk #3020 via ZenHub