Somatic
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Permissions on gs://broad-references0 votes 4 comments
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Mutect2 does not need normal BAM anymore?0 votes 5 comments
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Mutect2 - somatic variant calling with/without matched normal sample1 vote 14 comments
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Broad hg38 ICE interval list Answered3 votes 17 comments
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UnifiedGenotyper error on Solid data0 votes 2 comments
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Mutect2: Incorrectly computed allelic depths and likely false-positive calls0 votes 11 comments
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Mutect2 : annotation group & fields that can check strand bias0 votes 1 comment
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MergeBamAlignment Error: ArrayIndexOutOfBoundsException1 vote 3 comments
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Joint calling on individual gvcfs vs merged gvfs0 votes 1 comment
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Wrong Calculation of DP, AD, AF0 votes 8 comments
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alt_allele_in_normal vs normal LOD: Is alt_allele_in_normal redundant?0 votes 1 comment
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Filtering somatic calls from tumor-only variant calling0 votes 3 comments
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Artefactual calls using Mutect2 on RNAseq data Answered0 votes 25 comments
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calculateContamination step with multi-tumor samples0 votes 8 comments
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FilterMutectCalls does not actually filter mutations. Only flag them.0 votes 2 comments
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Mutect2 filter : clustered_events definition0 votes 5 comments
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Problems combining gVCFs that have thousands of scaffolds1 vote 5 comments
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Error in FilterMutectCalls0 votes 3 comments
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Mutect2: STR flag from INFO Field is not applied to multiallelic sites0 votes 4 comments
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Having trouble using LiftoverVcf due to value not being in VCF Header0 votes 1 comment
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JAVA errors from gnomad resource in Mutect2 Answered0 votes 2 comments
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Multi-mapping reads causing errors in Mutect2 for RNAseq?0 votes 3 comments
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HS_PENALTY_20X is -1 on one version of GATK, crashes on newest version.0 votes 1 comment
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Installation of GenomeSTRiP on slurm0 votes 6 comments
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Mutect2 doesn't output normal sample name in VCF?0 votes 3 comments