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MarkduplicatesSpark failed Answered0 votes 3 comments
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Contamination calculation on single file don't detect contaminated samples Answered0 votes 7 comments
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GenomincsDBImport Failed to create reader from file: An index is required, but none found., for input source: Answered0 votes 6 comments
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markduplicatesSpark .bam.parts output error (directory already exists) Answered0 votes 3 comments
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Funcotator gnomAD MAF columns Answered0 votes 2 comments
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Can't explain the number of reads FilterSamReads outputs Answered0 votes 8 comments
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GenomeSTRiP SVPreprocess failed Answered0 votes 3 comments
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Hi Can you please point me to the chain file for human_g1k_v37_decoy to hg19 conversion Answered0 votes 1 comment
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Docker image for GATK3 version 3.7 Answered0 votes 2 comments
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Funcotator missing cDNA, Codon, and Protein Change for some chromosomes Answered0 votes 1 comment
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Picard liftover Issue bostau8 to bostau6 Answered0 votes 2 comments
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DepthOfCoverage with -gene-list and readgroup as --partition-type options Answered0 votes 7 comments
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Mitochondrial analysis - FilterMutectCalls autosomal-coverage is not an option Answered0 votes 3 comments
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Mutect2: NuMTs filtering on RNA-seq Answered0 votes 2 comments
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Call-caching not functional running cromwell locally on GCP VM Answered0 votes 9 comments
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No results of CollectvariantCallingMetrics Answered0 votes 26 comments
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Truncated bam file after running ReplaceSamHeader(Picard) Answered0 votes 6 comments
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Confusing GVCF results Answered0 votes 1 comment
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Warning: Reading will be unbuffered. Answered1 vote 3 comments
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How to reduce the processing time of BwaMemIndexImageCreator Answered0 votes 2 comments
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evaluation of the VCF file which is made using GATK Answered0 votes 2 comments
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SelectVariants v4.1.6.0 doesn't select the variants as expected Answered0 votes 8 comments
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DepthofCoverage GATK4.1.7.0 -gene-list Answered0 votes 15 comments
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Panel of Normals Documentation Answered1 vote 15 comments
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GenomeStrip SVPreprocess works with for a chromosome region; but fail for whole genome Answered0 votes 10 comments
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Variant Filtration - FS and SOR are not supported Answered0 votes 1 comment
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Known issue: old GATK forum inaccessible Answered2 votes 3 comments
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CNNScoreVariants carshes with java.lang.NullPointerException Answered1 vote 11 comments