Somatic
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java.lang.OutofMemoryError: GC overhead limit exceeded Answered0 votes 28 comments
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Mutect2 issue with --force-active: not all regions are active Answered1 vote 25 comments
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Artefactual calls using Mutect2 on RNAseq data Answered0 votes 25 comments
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Why do a clear expected variant not show up in the Mutect2 vcf file Answered0 votes 20 comments
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The depth of SNV/InDels calculated by Mutect2 in GATK4.2.0.0 is much lower than real sequencing depth, why? Answered0 votes 19 comments
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Empty final PON vcf file from 7 samples Answered0 votes 18 comments
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Broad hg38 ICE interval list Answered3 votes 18 comments
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Error while running ModelSegments Answered0 votes 15 comments
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Mutect2 PoN - GenomicsDBImport creates empty DB Answered0 votes 15 comments
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Creating Panel of Normals (PoN) from Blood Sample of cancer patients Answered1 vote 14 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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Problems in subsampling reads for Mutect2 with --max-reads-per-alignment-start Answered1 vote 13 comments
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Funcotator data source not correct Answered0 votes 13 comments
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Picard Liftover hg38 to hg19 Error. Answered0 votes 13 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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CollectAllelicCounts- Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded Answered0 votes 12 comments
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FilterMutectCalls 'haplotype' filter value assigned to variants with different PGT tag Answered0 votes 10 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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The output of Mutect2 cannot be accepted by FilterMutectCalls in GATK-4.2.0.0 Answered0 votes 10 comments
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CreateSomaticPanelOfNormals ALT allele bug Answered0 votes 10 comments
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[Repost] Wrong annotation with Funcotator 1.7 Answered0 votes 10 comments
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FilterMutectCalls chokes on infinite POPAF produced by Mutect2 Answered0 votes 10 comments
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FilterMutectCalls, --distance-on-haplotype and variants filtered for haplotype Answered0 votes 9 comments
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How to decrease the likelihood threshold for a candidate haplotype to be called as a genotype in Mutect2 Answered0 votes 9 comments
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A USER ERROR has occurred: af-only-gnomad.hg38.vcf.gz because no suitable codecs found Answered0 votes 9 comments
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AnalyzeCovariates Answered0 votes 9 comments
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Mysterious Funcotator issue Answered0 votes 8 comments
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Mutect2 - Joint calling Answered0 votes 8 comments
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Error initializing feature reader for path somatic-hg38_1000g_pon.hg38.vcf.gz Answered0 votes 8 comments
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How mutect2 panel of normal works? Answered0 votes 8 comments