Somatic
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The mutect ERROR：Please add an explicit type tag :NAME listing the correct type from among the supported types Answered0 votes 3 comments
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Error while running CreateReadCountPanelOfNormals with gatk-4.1.4.1 Answered0 votes 3 comments
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MuTect2 Mismatch between the reference haplotype and the reference assembly graph path. Answered0 votes 1 comment
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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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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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How do I set less stringent germline filtering in Mutect2 / filtermutectcalls, many false negatives Answered0 votes 1 comment
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Mysterious Funcotator issue Answered0 votes 7 comments
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MergeBamAlignment produces unknown error Answered0 votes 4 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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IlluminaBasecallsToSam does not demultiplex NovaSeq barcoded reads Answered0 votes 5 comments
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java.lang.OutofMemoryError: GC overhead limit exceeded Answered0 votes 28 comments
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GenomicsDBImport does not support GVCFs with MNPs Answered0 votes 1 comment
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Mutect20 votes 1 comment
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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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CreateSomaticPanelOfNormals ALT allele bug Answered0 votes 10 comments
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Funcotator data source not correct Answered0 votes 13 comments
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Issue Regarding CNV_Somatic_Pair Workflow0 votes 0 comments
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Mutect2 failing to produce F1R2.tar.gz files on TCGA bam (tumor-normal pairs) Answered0 votes 5 comments
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Variant called in reads from ArtificialHaplotypeRG Answered0 votes 4 comments
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Picard CrosscheckFingerprint: Sequence dictionaries are not the same size Answered0 votes 3 comments
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FilterAlignmentArtifacts - only emitting PASS variants Answered0 votes 3 comments
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Missing documentation on strict_strand Answered0 votes 4 comments
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strand_bias filtering is never emitted Answered0 votes 7 comments
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FilterMutectCalls didn't filtered any variants for my vcf file Answered0 votes 3 comments
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Mutect2 - Joint calling Answered0 votes 8 comments
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HaplotypeCaller VCF for PON0 votes 3 comments
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Bug: Badly formed genome unclippedLoc0 votes 10 comments
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FilterMutectCalls --unique-alt-read-count argument0 votes 10 comments