1. Community
2. Somatic
3. alt_allele_in_normal vs normal LOD: Is alt_allele_in_normal redundant?

Cheng Yan alt_allele_in_normal is a filter from an old version of Mutect2.  Only the probabilistic normal artifact model remains.

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• David Benjamin
• February 18, 2020 17:59
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1. Community
2. Somatic
3. Filtering somatic calls from tumor-only variant calling

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...

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• David Benjamin
• February 18, 2020 16:59
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1. Community
2. Other
3. What is the 'physical phasing'

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...

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• David Benjamin
• February 18, 2020 16:52
• 0 votes