Somatic
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How to set neutral-segment-copy-ratio for somatic CNV calling0 votes 5 comments
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Funcotator b37 and hg19 contig compatibility issue0 votes 5 comments
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Singularity Modifications to wdl file0 votes 1 comment
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(GATK v4.1.6.0) Mutect2 bamout reports fewer reads than VCF AD0 votes 1 comment
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CNV not called in some samples0 votes 4 comments
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Picard Liftover hg38 to hg19 Error. Answered0 votes 13 comments
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Somatic mosaic variants0 votes 1 comment
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Chromosome name of db SNP hg38 build for Funcotator0 votes 4 comments
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BaseRecalibrator raised htsjdk.tribble.TribbleException$MalformedFeatureFile0 votes 12 comments
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Mutect2 not calling a 4-bp deletion in BRCA1 with 50% AF0 votes 7 comments
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Combining gVCFs containing MNPs is not supported for Ploidy Samples0 votes 4 comments
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Calling somatic multi-nucleotide polymorphisms with Mutect20 votes 3 comments
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Mutect2 filter somatic mutations as multiallelic and clustered_events0 votes 2 comments
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GenomeSTRiP SVGenotyping script and alt allele alignment0 votes 4 comments
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Same fastqs and pipeline get different results0 votes 2 comments
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GATK4.1.5 mutect2 output issue0 votes 5 comments
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Somatic CNV hypersegmentation introduced by PoN0 votes 4 comments
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Parameter tuning in Mutect20 votes 1 comment
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Funcotator: VCF output0 votes 2 comments
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Interpretting CrosscheckFingerprints metrics0 votes 12 comments
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Mutect2 include MNPs0 votes 5 comments
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Panel of Normals index files not found0 votes 1 comment
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Stalled Shards0 votes 1 comment
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Mutect2 - Bad input: GenomicsDBImport does not support GVCFs with MNPs0 votes 1 comment
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How to compensate for absence of normals for few samples?0 votes 2 comments
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Output files can't be found0 votes 6 comments
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Scatter Count recommendations0 votes 1 comment
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about Mutect2 usage0 votes 3 comments
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gnomAD version in Mutect2 bundle0 votes 4 comments