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Out of memory error using OpenJDK vs Oracle JDK for CNV-LOH2 votes 2 comments
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Known issue: old GATK forum inaccessible Answered2 votes 3 comments
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Any automatic downloadable gatk3?2 votes 13 comments
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HaplotypeCaller -ERC GVCF -variant_index_type LINEAR1 vote 1 comment
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How do I rename output folder created using glob (WDL-Cromwell)?1 vote 1 comment
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GenomicsDBImport: Attempting to genotype more than 50 alleles1 vote 2 comments
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GenomicsDBImport: has too many genotypes in the combined VCF record1 vote 2 comments
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Warning: Reading will be unbuffered. Answered1 vote 3 comments
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Picard CollectHsMetrics PCT_EXC_OFF_TARGET1 vote 4 comments
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Problem Installing and testing GATK-4.1.7.01 vote 5 comments
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Do I need to perform fastqc and adapters trimming before gatk pipeline?1 vote 4 comments
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jar for mutect 1.1.71 vote 6 comments
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Panel of Normals Documentation Answered1 vote 15 comments
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GATK/Picard does not detect mates in paired-end BAM1 vote 3 comments
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HaplotypeCaller produces very large .idx files1 vote 4 comments
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ValidateSamFile behavior1 vote 7 comments
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Problem Installing GATK python environment - SOLUTION POSTED! Featured1 vote 17 comments
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Typos in docs1 vote 1 comment
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CNNScoreVariants carshes with java.lang.NullPointerException Answered1 vote 11 comments
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MarkDuplicatesSpark crash1 vote 9 comments
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CollectRnaSeqMetrics GL000220 test not counting ribosomal reads0 votes 3 comments
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MarkduplicatesSpark failed Answered0 votes 3 comments
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Dictionary cannot have size zero error0 votes 1 comment
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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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HaplotypeCaller inconsistency with different interval lists0 votes 5 comments
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My recalibration table from BaseRecalibrator is empty0 votes 5 comments