Somatic
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Panel of normal issue0 votes 2 comments
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Funcotator: Unable to open SQLite DB for COSMIC Answered0 votes 7 comments
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ModelSegments not reading allelic counts file Answered0 votes 1 comment
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Error "Could not create tar.gz file" for Mutect2 --f1r2-tar-gz0 votes 3 comments
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ModelSegments - java.lang.IllegalArgumentException: Metadata of the allelic counts and the segments do not match Answered0 votes 3 comments
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Error in building panel of normal in somatic copy number variation calling Answered0 votes 4 comments
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Contig chr1_KQ031383v1_fix not present in the sequence dictionary Answered0 votes 5 comments
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How to create Panel of Normals?0 votes 7 comments
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FilterMutectCalls 'haplotype' filter value assigned to variants with different PGT tag Answered0 votes 9 comments
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A USER ERROR has occurred: Duplicate sample: PD4086bv2. Sample was found in both file Answered0 votes 7 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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FilterMutectCalls, --distance-on-haplotype and variants filtered for haplotype Answered0 votes 9 comments
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Read-orientation filter removes tens of thousands of somatic variants after FilterMutectCalls Answered0 votes 6 comments
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Baserecalibarator error: half of the files worked without any error Answered0 votes 1 comment
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Mutect2 unexpected false negative due to changes in smith-waterman parameters? Answered0 votes 3 comments
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Mutect2 missing a low AF known deletion0 votes 4 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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mutect2.bam could not find the mutation, but bqsr found the mutation Answered0 votes 1 comment
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mutect2 genotyping wrong? Answered0 votes 1 comment
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Mutect stats table not found.0 votes 1 comment
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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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GGA-mode gives PASS tag while the site failed in the normal workflow0 votes 13 comments
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Error while running ModelSegments Answered0 votes 3 comments
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Mutect2 Funcotator interval error Answered0 votes 5 comments
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Called Somatic Mutations High Frequency of C>A SNVs Answered0 votes 6 comments
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empty pon vcf file Answered1 vote 1 comment
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Funconator's ignore-filtered-variants is not a recognized option Answered0 votes 1 comment
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missing file: Callset.json , when creating PON Answered0 votes 3 comments
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MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true does not add DS and DI tags in the output BAM file Answered0 votes 3 comments