Somatic
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strand bias and orientation bias4 votes 1 comment
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Broad hg38 ICE interval list Answered3 votes 17 comments
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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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Problems in subsampling reads for Mutect2 with --max-reads-per-alignment-start Answered1 vote 13 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 active Answered1 vote 25 comments
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Broad hg19 TWIST interval list Answered1 vote 4 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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ModelSegments not reading allelic counts file Answered0 votes 1 comment
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Error "Could not create tar.gz file" for Mutect2 --f1r2-tar-gz0 votes 3 comments
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ModelSegments - java.lang.IllegalArgumentException: Metadata of the allelic counts and the segments do not match Answered0 votes 3 comments
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Error in building panel of normal in somatic copy number variation calling Answered0 votes 4 comments
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Contig chr1_KQ031383v1_fix not present in the sequence dictionary Answered0 votes 5 comments
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How to create Panel of Normals?0 votes 7 comments
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FilterMutectCalls 'haplotype' filter value assigned to variants with different PGT tag Answered0 votes 9 comments
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A USER ERROR has occurred: Duplicate sample: PD4086bv2. Sample was found in both file Answered0 votes 7 comments
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In Mutect2 force-calling allele via --alleles does not force-call the allele Answered0 votes 14 comments
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FilterMutectCalls, --distance-on-haplotype and variants filtered for haplotype Answered0 votes 9 comments
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Read-orientation filter removes tens of thousands of somatic variants after FilterMutectCalls Answered0 votes 6 comments