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Hi, FilterAlignmentArtifacts only emits PASS variants. Is this expected behavior? I would expect it would just add 'alignment' filter and output all variants. Otherwise it prevents users from fine-...

• GE
• March 01, 2021 15:38
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2. Somatic

Hi, The strict_strand filter in FilterMutectCalls is listed in the output VCF header regardless of whether it is actually applied, but it is only applied when the --min-reads-per-strand setting is ...

• GE
• February 28, 2021 19:15
• Edited
• 2 followers
• 4 comments
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2. Somatic

Hi, I am running Mutect2 4.1.9.0 using the latest Terra pipeline. Although in the VCF header, the strand_bias FILTER is listed, it is never applied to any variants across 5 different samples. At th...

• GE
• February 28, 2021 18:11
• Edited
• 4 followers
• 7 comments
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Hi, See this bug on github: https://github.com/broadinstitute/gatk/issues/5690 It has been 1 year and still not fixed. It affects all tools that use smith waterman alignment from libgkl. Errors sti...

• GE
• February 18, 2021 23:16
• 3 followers
• 3 comments
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2. Somatic

Hi, I'm getting this error: A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "combinedblacklist.intervallist" is not valid for this input In Mutect2. The file is being pa...

• GE
• February 16, 2021 22:43
• 4 followers
• 12 comments
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2. Documentation Questions

Hi, What are the types of pedigree relationships that CalculateGenotypePosteriors can employ? The documentation seems to suggest only parents relationships, but it isn't clear. For example, what if...

• GE
• February 10, 2020 22:54
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• 1 comment
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