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Error in running SplitNCigarReads - htsjdk.samtools.util.RuntimeIOException Answered0 votes 9 comments
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Liftover Picard hg19 to hg38: variants were not successfully lifted over Answered2 votes 3 comments
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GATK Index Feature FIle No suitable codecs found Answered0 votes 4 comments
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Install GATK version 4.1.0.0 using Conda. Answered0 votes 4 comments
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BaseRecalibrator on MT .bam files Answered0 votes 5 comments
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evaluation of the VCF file which is made using GATK Answered0 votes 6 comments
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MergeVcfs issue: Illegal character in fragment at index 1: ##fileformat=VCFv4.2 Answered0 votes 2 comments
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Invalid or corrupt jarfile error Answered0 votes 2 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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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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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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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 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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No results of CollectvariantCallingMetrics Answered0 votes 30 comments
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CNNScoreVariants carshes with java.lang.NullPointerException Answered1 vote 13 comments
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CNNScoreVariants Issues with environment and Java version Answered0 votes 6 comments
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ApplyBQSR no positional argument is defined for this tool Answered0 votes 7 comments
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Fontconfig error in the newest gatk docker image Answered0 votes 1 comment