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User error: input files reference and features have incompatible contigs0 votes 6 comments
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Loss of data after HaplotypeCaller0 votes 5 comments
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What is the 'physical phasing'0 votes 3 comments
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Cannot get AddOrReplaceReadGroups to run0 votes 2 comments
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Where's the DRAGEN?0 votes 3 comments
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PathseqPipelineSpark stops without error message0 votes 6 comments
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GATK on Oracle Cloud Infrastructure0 votes 2 comments
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Problem Installing GATK python environment - SOLUTION POSTED! Featured1 vote 17 comments
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GenomeStrip SVPreprocess works with for a chromosome region; but fail for whole genome Answered0 votes 10 comments
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options used during base recalibration0 votes 6 comments
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Typos in docs1 vote 1 comment
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GATK Workshop Registration Details0 votes 3 comments
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Run ReorderSam faster with0 votes 1 comment
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Vcf-annotate does not work0 votes 1 comment
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AS_MQRanksum craches R script VQSR0 votes 8 comments
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Variant Filtration - FS and SOR are not supported Answered0 votes 1 comment
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Where to find old discussion0 votes 2 comments
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Known issue: old GATK forum inaccessible Answered2 votes 3 comments
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CNNScoreVariants carshes with java.lang.NullPointerException Answered1 vote 11 comments
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Feature request: Restore the StrandAlleleCount annotation from GATK30 votes 2 comments
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Any automatic downloadable gatk3?2 votes 13 comments
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MarkDuplicatesSpark crash1 vote 9 comments