Somatic
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Details about the filters used in a previous version of FilterMutectCalls0 votes 7 comments
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Mutect2 output False Negative SNV result0 votes 6 comments
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Mutect2 overlapping reads behavior with --pcr-snv-qual parameter0 votes 2 comments
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Mutect2 -could not detect expected Indels0 votes 2 comments
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SOLVED: Get read counts of Mutect2 somatic variants1 vote 1 comment
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Why are some variants not phased in Mutect20 votes 1 comment
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CalculateContamination error0 votes 1 comment
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how to generate the common site file for hg38 (CNV analysis)0 votes 2 comments
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False positive INDELs by Mutect20 votes 1 comment
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Error using output of ScatterIntervalsByNs by SplitIntervals0 votes 4 comments
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Mutect2 with HiFi0 votes 2 comments
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Mutect2 - No .stats file created with SLURM1 vote 2 comments
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How to recover a mutation from secondary alignment0 votes 8 comments
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Creating Panel of Normals (PoN) from Blood Sample of cancer patients Answered1 vote 14 comments
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Somatic copy number variants (CNVs) and Panel of Normals creation0 votes 6 comments
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Mutect2 multi-sample pipeline0 votes 15 comments
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MUTECT2 bamout reports far more reads than original bam - reliable?0 votes 1 comment
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normal sample AF in Mutect2 paired mode0 votes 1 comment
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FilterMutectCalls complains about the --ob-prior file's result0 votes 4 comments
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SNP analysis returning way too many variants0 votes 2 comments
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No headers found in VCF0 votes 6 comments
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Why do a clear expected variant not show up in the Mutect2 vcf file Answered0 votes 20 comments
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Missing mutations0 votes 11 comments
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mutect2.bam could not find the mutation, but bqsr found the mutation Answered0 votes 2 comments
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strand bias and orientation bias5 votes 2 comments