Somatic
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strand bias and orientation bias5 votes 2 comments
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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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SOLVED: Get read counts of Mutect2 somatic variants1 vote 1 comment
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Mutect2 - No .stats file created with SLURM1 vote 2 comments
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GATK Muteck2 missing call Answered1 vote 2 comments
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Funcotator maf has different alt allele than vcf for some variants1 vote 1 comment
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Creating Panel of Normals (PoN) from Blood Sample of cancer patients Answered1 vote 14 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 calls long deletion with absolutely zero read support Answered1 vote 3 comments
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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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Details about the filters used in a previous version of FilterMutectCalls0 votes 7 comments
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Mutect2 overlapping reads behavior with --pcr-snv-qual parameter0 votes 2 comments