Somatic
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GATK 4.3.0.0 Mutect2 fail to call variant Answered0 votes 2 comments
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Panel of Normals creation error: GenomicsDBImport does not support GVCFs with MNPs Answered0 votes 1 comment
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GATK Muteck2 missing call Answered1 vote 2 comments
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Mutect2 cannot generate stats file and f1r2.tar.gz file Answered0 votes 4 comments
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Picard error (AddOrReplaceReadGroups) Answered0 votes 4 comments
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Funcotator error: Only IGRs were produced for this dataset Answered0 votes 4 comments
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improt gcnvkernel fails. somehting to do with theano lock Answered0 votes 3 comments
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Difference between variants detected using gatk 4.1.8.1 and 4.1.9.0 Answered0 votes 2 comments
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GenotypeGVCFs Answered0 votes 1 comment
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GATK4 ModelSegment Error Allelic-count sites must be identical across all samples Answered0 votes 2 comments
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Combine two panel-of-normals files Answered0 votes 2 comments
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Creating Panel of Normals (PoN) from Blood Sample of cancer patients Answered1 vote 14 comments
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Panel of normal issue Answered0 votes 1 comment
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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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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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FilterMutectCalls 'haplotype' filter value assigned to variants with different PGT tag Answered0 votes 10 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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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 2 comments
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mutect2 genotyping wrong? Answered0 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