Somatic
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Mutect2 genotype-germline-sites filtering discrepancy Answered0 votes 6 comments
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missing file: Callset.json , when creating PON Answered0 votes 5 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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Why do a clear expected variant not show up in the Mutect2 vcf file Answered0 votes 20 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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GATK 4.3.0.0 Mutect2 fail to call variant Answered0 votes 2 comments
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Mysterious Funcotator issue Answered0 votes 8 comments
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FilterMutectCalls 'haplotype' filter value assigned to variants with different PGT tag Answered0 votes 10 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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Error while running ModelSegments Answered0 votes 15 comments
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Funcotator error: Only IGRs were produced for this dataset Answered0 votes 4 comments
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Mutect2 cannot generate stats file and f1r2.tar.gz file Answered0 votes 4 comments
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GATK Muteck2 missing call Answered1 vote 2 comments
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Picard error (AddOrReplaceReadGroups) 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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Mutect2 filter : clustered_events definition Answered0 votes 7 comments
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Mutect2 calls long deletion with absolutely zero read support Answered1 vote 3 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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Panel of normal issue Answered0 votes 1 comment
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Empty final PON vcf file from 7 samples Answered0 votes 18 comments
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Funcotator: Unable to open SQLite DB for COSMIC Answered0 votes 7 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 19 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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In Mutect2 force-calling allele via --alleles does not force-call the allele Answered0 votes 14 comments
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Contig chr1_KQ031383v1_fix not present in the sequence dictionary Answered0 votes 5 comments