New User Advice
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Error, ShouldNeverReachHereException, FuncotationMap in FilterFuncotations Answered0 votes 20 comments
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GATK GenomicsDBImport intervals Answered0 votes 19 comments
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ReadsPipelineSparkMulticore.wdl, Unrecognized runtime attribute keys: discs, cpu Answered0 votes 13 comments
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ValiidateSamFile Error: Mate not found Answered0 votes 13 comments
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Steps For GATK-gCNV pipleline on Exome Data0 votes 12 comments
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ApplyBQSR0 votes 10 comments
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VCF file SNP ID missing0 votes 9 comments
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Empty intersection error when applying intervals Answered0 votes 8 comments
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ApplyBQSR for somatic mutation detection in HLA regions Answered0 votes 7 comments
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DP for each variant bulk is skewed towards 50 and multiples of 500 votes 7 comments
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CollectInsertSizeMetrics can't find R0 votes 6 comments
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Unclear why Picard ValidateSamFile is producing an error Answered0 votes 6 comments
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Using GATK as a genotyper to genotype existing variants Answered0 votes 6 comments
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GATK MarkDuplicates Missing output file1 vote 5 comments
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GATK configration0 votes 5 comments
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Markduplicates0 votes 5 comments
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A USER ERROR has occurred: Contig chr1_KI270762v1_alt not present in reads sequence dictionary Answered0 votes 5 comments
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Somatic mutation detection in HLA regions using hg38 alt-aware alignments Answered0 votes 5 comments
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Estimate genotype proportions from filtered variants0 votes 5 comments
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Help with WDL workflow for mutec2? Answered0 votes 5 comments
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Running best practices workflow step-by-step in command line1 vote 5 comments
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Find rate of homozygosity Answered0 votes 4 comments
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Suggestions to find pathogenic variant Answered0 votes 4 comments
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How to provide custom exon-intron annotation source in Funcotator0 votes 4 comments
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GATK4.0.3.0 - CombineGVCFs - Unexpected base in allele bases0 votes 4 comments
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Whole Genome pipe for use with non whole genome data0 votes 3 comments
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Issue with Running MuTect in GATK Version Compatibility0 votes 3 comments