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BaseRecalibrator on MT .bam files0 votes 1 comment
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LiftoverVcf: hg19 to hg38 all variants mismatched0 votes 3 comments
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Checking ReadGroup name in BAM file with GATK instructions0 votes 1 comment
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How to work with CNN variant caller0 votes 3 comments
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Mitochondrial analysis - FilterMutectCalls autosomal-coverage is not an option Answered0 votes 3 comments
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HaplotypeCaller and Read Group Errors0 votes 1 comment
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filterSamReads stdout format error0 votes 15 comments
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Cromwell stuck at WaitingForReturnCode on Mac0 votes 3 comments
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Reference Fasta vs Alt Reference Fasta0 votes 2 comments
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Mutect2: NuMTs filtering on RNA-seq Answered0 votes 2 comments
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Comparison between ReadsPipelineSpark and MarkDuplicates0 votes 7 comments
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Resource bundle for GRCh370 votes 2 comments
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Funcotator missing AF0 votes 1 comment
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MarkDuplicates0 votes 1 comment
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ASEReadCounter java.lang.ArrayIndexOutOfBoundsException: 00 votes 3 comments
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Any documents for 199 columns in Funcotator output?0 votes 2 comments
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How to merge approx 150 bam file using Picard0 votes 4 comments
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DepthOfCoverage in GATK4.1.9.0 with -gene-list option0 votes 4 comments
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Clarity on Variant Callers being "optimized for UMI-containing data"0 votes 1 comment
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BQSR no output table found0 votes 3 comments
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How do I get intermediate outputs from cromwell0 votes 1 comment
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Missing ReadPosRankSum, MQRankSum and BaseQRankSum Scores in VCF0 votes 1 comment
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Call-caching not functional running cromwell locally on GCP VM Answered0 votes 9 comments
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HaplotypeCaller - Shutting down engine - Encountering a large genome0 votes 5 comments