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VCF input example Answered0 votes 1 comment
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Cannot use haplotype caller on STAR-aligned data Answered0 votes 2 comments
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MergeVcfs issue: Illegal character in fragment at index 1: ##fileformat=VCFv4.2 Answered0 votes 1 comment
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FindBadGenomicKmersSpark running indefinitely Answered0 votes 5 comments
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Using the IndexFeatureFile, doesn't recognize -F flag Answered0 votes 2 comments
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GenomicsDBImport works in interactive shell, but not in a script Answered0 votes 1 comment
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Haploytpe caller shows me that 0 read(s) were filtered by: MappingQualityAvailableReadFilter etc. Answered0 votes 4 comments
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How to run muTect without normal sample? Answered1 vote 3 comments
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markDuplicatesSpark running out of memory Answered0 votes 3 comments
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Hard filters on VariantFiltration following HaplotypeCaller; Filter contains an illegal character Answered0 votes 5 comments
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Refseq accession number and version number in Funcotator Answered0 votes 4 comments
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CNNScoreVariants Issues with environment and Java version Answered0 votes 6 comments
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Fontconfig error in the newest gatk docker image Answered0 votes 1 comment
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vulnerability issue for gatk-package-4.2.5.0-local.jar Answered0 votes 4 comments
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Local WDL Mitochondria Pipeline - Import failed Answered0 votes 1 comment
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Error in GenomicsDBImport: Invalid deflate block found Answered1 vote 6 comments
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GC overhead limit exceeded using Mutect2 only tumor version Answered0 votes 5 comments
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GATK R plots with R v4.1.2 Answered0 votes 3 comments
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Error in running GenomicsDBConfigException Answered0 votes 12 comments
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CollectRnaSeqMetrics GL000220 test not counting ribosomal reads Answered0 votes 5 comments
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MarkduplicatesSpark failed Answered0 votes 5 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