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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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How do I rename output folder created using glob (WDL-Cromwell)?1 vote 1 comment
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Where do I find guidance on when to mark duplicates a second time?1 vote 1 comment
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VQSR in variants on X chromosome1 vote 2 comments
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Cromwell support for n2 and n2d instance types in GCP1 vote 2 comments
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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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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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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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GATK Best Practices Mitochondrial Analysis1 vote 29 comments
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MarkDuplicatesSpark crash1 vote 9 comments
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BaseRecalibrator on MT .bam files0 votes 1 comment
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LiftoverVcf: hg19 to hg38 all variants mismatched0 votes 3 comments
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Checking ReadGroup name in BAM file with GATK instructions0 votes 1 comment
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How to work with CNN variant caller0 votes 3 comments
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HaplotypeCaller and Read Group Errors0 votes 1 comment