Somatic
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GGA-mode gives PASS tag while the site failed in the normal workflow0 votes 13 comments
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Error while running ModelSegments Answered0 votes 3 comments
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Mutect2 Funcotator interval error Answered0 votes 5 comments
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Called Somatic Mutations High Frequency of C>A SNVs Answered0 votes 6 comments
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empty pon vcf file Answered1 vote 1 comment
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Funconator's ignore-filtered-variants is not a recognized option Answered0 votes 1 comment
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missing file: Callset.json , when creating PON Answered0 votes 3 comments
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MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true does not add DS and DI tags in the output BAM file Answered0 votes 3 comments
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SAMException: Value was put into PairInfoMap more than once Answered0 votes 5 comments
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Why do I see a variant called by mutect2 in my matched-normal sample when checking the results? Answered0 votes 10 comments
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Mutect2 calls long deletion with absolutely zero read support Answered0 votes 1 comment
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Deletion is split into two deletions Answered0 votes 1 comment
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Running Mutect 2 with matched normal vs tumor mode0 votes 3 comments
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Why do I get 'java.lang.IllegalArgumentException: Dictionary cannot have size zero' when using GetPileupSummaries? Answered0 votes 12 comments
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Not generating denoisedLimit4.png with PlotModeledSegments0 votes 4 comments
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Mutect2 issue with --force-active: not all regions are active Answered1 vote 25 comments
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Incorrect Annotation from Funcotator Answered0 votes 5 comments
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merge nearby variants in vcf from mutect2 Answered0 votes 1 comment
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gatk stack memory insufficient to run Mutect2 for artifact correction Answered0 votes 1 comment
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Mutect2 genotype-germline-sites filtering discrepancy Answered0 votes 4 comments
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Error running mutect2 on SAM files remapped to hg38 (original reads were aligned to hg19). Answered0 votes 1 comment
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Missing Variants from Panel of Normals Answered0 votes 2 comments
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GetPileupSummaries Answered0 votes 5 comments
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Mutect2 PoN - GenomicsDBImport creates empty DB Answered0 votes 15 comments
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Created panel of normals returns empty vcf Answered0 votes 3 comments
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selecting allele depth Mutect2 Answered0 votes 1 comment
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The mutect ERROR：Please add an explicit type tag :NAME listing the correct type from among the supported types Answered0 votes 3 comments
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Error while running CreateReadCountPanelOfNormals with gatk-4.1.4.1 Answered0 votes 3 comments