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CommentsVotes on activity by David Benjamin Sort by votes
Cheng Yan alt_allele_in_normal is a filter from an old version of Mutect2. Only the probabilistic normal artifact model remains.
By default, Mutect2 skips obvious germline variants and only sends cases to mild doubt to FilterMutectCalls. --genotype-germline-sites disables that optimization and tells Mutect2 to go through th...
whynot Two or more variants that are close enough for HaplotypeCaller to attempt to phase share a PID tag. Within a set of variants with the same PID, the PGT tells us which of two homologous chro...