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Invalid or corrupt jarfile error0 votes 1 comment
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Does GATK4 BaseRecalibrator not understand relative paths?0 votes 10 comments
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HaplotypeCaller confuses introns as long deletions0 votes 2 comments
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CombineGVCFs - possible to restart/continue run?0 votes 5 comments
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error when running ASEReadCounter0 votes 2 comments
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SortSam - Question about I/O error0 votes 2 comments
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Broken: conda env create -n gatk -f gatkcondaenv.yml0 votes 17 comments
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ShiftFasta creates empty intervals file Answered0 votes 4 comments
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Error in Running command CreateExtendedIlluminaManifest Answered0 votes 3 comments
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Accessing the resource bundle. Answered0 votes 6 comments
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CGA3_WES_Characterization_Pipeline_v0.2_Jun2019 PoN Errors...0 votes 1 comment
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How can I build the GATK jar so that the intel native libraries are available? Answered0 votes 4 comments
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libgkl_compression.so not found + Failed to detect Google Compute Engine in a GATK workflow Answered0 votes 4 comments
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How to run muTect without normal sample? Answered1 vote 3 comments
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GenomeSTRiP SVPreprocess error1 vote 1 comment
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VCF input example Answered0 votes 1 comment
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GenomicsDBImport: Attempting to genotype more than 50 alleles Answered1 vote 9 comments
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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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MarkduplicatesSpark failed Answered0 votes 5 comments
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MarkDuplicatesSpark crash1 vote 10 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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HaplotypeCaller complains (in 2 different ways) about sample-name0 votes 12 comments
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Refseq accession number and version number in Funcotator Answered0 votes 4 comments
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No results of CollectvariantCallingMetrics Answered0 votes 30 comments