Somatic
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Mutect2 Funcotator error0 votes 31 comments
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Mutect2-PON Storage object issue when running across multiple samples?0 votes 30 comments
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java.lang.OutofMemoryError: GC overhead limit exceeded Answered0 votes 28 comments
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Funcotator errors0 votes 27 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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The depth of SNV/InDels calculated by Mutect2 in GATK4.2.0.0 is much lower than real sequencing depth, why? Answered0 votes 18 comments
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Mutect2 PON - gnomAD input?0 votes 18 comments
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Empty final PON vcf file from 7 samples0 votes 17 comments
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CalculateContamination: Multiple KernelSegmenter warnings0 votes 17 comments
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Mutect2 doesn't produce stats file0 votes 17 comments
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Broad hg38 ICE interval list Answered3 votes 17 comments
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Mutect2 PoN - GenomicsDBImport creates empty DB Answered0 votes 15 comments
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Mutect2 MISSING Low Frequency key (TP53 and KRAS) mutations1 vote 15 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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Mutect2 - somatic variant calling with/without matched normal sample1 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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GGA-mode gives PASS tag while the site failed in the normal workflow0 votes 13 comments
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Funcotator data source not correct Answered0 votes 13 comments
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Mutect2 multi-sample pipeline0 votes 13 comments
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Option "--dont-use-soft-clipped-bases" does not seem to work in Mutect20 votes 13 comments
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Increased number of false positives in Mutect2 GATK 4.1.7.00 votes 13 comments
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Picard Liftover hg38 to hg19 Error. Answered0 votes 13 comments
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Mutect2 - Need one or two reads to construct a fragment0 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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Why do a clear expected variant not show up in the Mutect2 vcf file Answered0 votes 12 comments
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Issues with Java heap space in CollectAllelicCounts0 votes 12 comments
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BaseRecalibrator raised htsjdk.tribble.TribbleException$MalformedFeatureFile0 votes 12 comments
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Interpretting CrosscheckFingerprints metrics0 votes 12 comments