yqiu
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Problems in subsampling reads for Mutect2 with --max-reads-per-alignment-start
AnsweredWe have a known variant with high AF (~0.3) and are trying to use Mutect2 to detect it. It can be called with no problem if we disable subsampling with "--max-reads-per-alignment-start 0". The var...
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Target variants not in active region
AnsweredWe have a known SNV with AF ~1% and are trying to use Mutect2 to detect it in amplicon sequencing data. It can be called with no problem in some samples but cannot be called in other samples. The...
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Mutect2 AF does not match AD and DP
AnsweredWe have one indel detected by Mutect2 but the AF reported does not match AD and DP. As shown below, AF is 0.425 and 0.134 for two alternative alleles. But AD is only 258 and 255 respectively with 1...
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Variants missing in 4.2.0.0 due to assembly cycles
AnsweredWe have a known SNV with AF ~1% and are trying to use Mutect2 to detect it in amplicon sequencing data. It can be called with GATK 4.1.8.1 without problems in multiple samples. It cannot be calle...