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Fail to set up conda environment for GATK with the gatkcondaenv.yml file0 votes 5 comments
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Question: Picard - MergeBamAlignment: Reads remaining on alignment iterator0 votes 4 comments
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HaplotypeCaller produces very large .idx files1 vote 4 comments
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What kind of statistical methods genome strip used?0 votes 3 comments
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HaplotypeCaller complains (in 2 different ways) about sample-name0 votes 8 comments
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Problem running GenomeSTRiP CNVDiscovery on X chromosome0 votes 5 comments
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BI and BD tags.0 votes 2 comments
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ValidateSamFile behavior1 vote 6 comments
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GRCh38 alignment0 votes 1 comment
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WES covarage analysis0 votes 4 comments
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<b>OUT OF OFFICE NOTICE</b>: GATK Team on holiday on Feb 17th 20200 votes 0 comments
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User error: input files reference and features have incompatible contigs0 votes 1 comment
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Loss of data after HaplotypeCaller0 votes 5 comments
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Could gatk tool: collectOxogMetrics accept CRAM input directly?0 votes 2 comments
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What is the 'physical phasing'0 votes 2 comments
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Cannot get AddOrReplaceReadGroups to run0 votes 2 comments
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Best Practice for Quantifying rRNA Content0 votes 1 comment
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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