Somatic
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strand bias and orientation bias2 votes 1 comment
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Custom made Panel of Normals required?2 votes 2 comments
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Generating ACS like output from new GATK CNV pipeline (WGS)2 votes 4 comments
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Broad hg38 ICE interval list Answered2 votes 17 comments
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empty pon vcf file Answered1 vote 1 comment
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Mutect2 issue with --force-active: not all regions are active1 vote 21 comments
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Broad hg19 TWIST interval list Answered1 vote 2 comments
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bwa index doesn't create .alt file in hg38 Answered1 vote 8 comments
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MarkDuplicatesSpark error missing Read Group fields1 vote 1 comment
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CalculateContamination "there is no such column: contig"1 vote 8 comments
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gatk CollectAllelicCounts error1 vote 6 comments
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Mutect2 MISSING Low Frequency key (TP53 and KRAS) mutations1 vote 15 comments
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Mutect2 - somatic variant calling with/without matched normal sample1 vote 14 comments
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MergeBamAlignment Error: ArrayIndexOutOfBoundsException1 vote 3 comments
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Problems combining gVCFs that have thousands of scaffolds1 vote 5 comments
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Call germline mutations from Mutect21 vote 3 comments
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Mutect stats table not found.0 votes 1 comment
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GGA-mode gives PASS tag while the site failed in the normal workflow0 votes 9 comments
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Error while running ModelSegments Answered0 votes 3 comments
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Mutect2 Funcotator interval error Answered0 votes 3 comments
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Called Somatic Mutations High Frequency of C>A SNVs0 votes 6 comments
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Funconator's ignore-filtered-variants is not a recognized option0 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