Documentation Questions
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Known Sites for BQSR Answered5 votes 5 comments
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Difference between the different annotation groups available in GATK2 votes 1 comment
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Where is the list of annotations and annotation groups? Answered2 votes 7 comments
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gCNV2 votes 1 comment
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GATK4.1.5 GenotypeGVCFs --annotation-group2 votes 1 comment
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Report file CreateExtendedIlluminaManifest Report file1 vote 1 comment
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Limit core use of DetermineGermlineContigPloidy & GermlineCNVCaller Answered1 vote 1 comment
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Documentation for running GATK and Cromwell on IBM Cloud Answered1 vote 7 comments
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genotyping calls don't align with coverage Answered1 vote 1 comment
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Where do I find guidance on when to mark duplicates a second time? Answered1 vote 2 comments
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Germline Resouce Answered1 vote 3 comments
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CollectAllelicCounts interval_list Answered1 vote 15 comments
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vcf files for BQSR step Answered1 vote 4 comments
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GATK Best Practices Mitochondrial Analysis Answered1 vote 45 comments
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Picard's CollectRnaSeqMetrics0 votes 0 comments
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Detailed reason for filtering by FilterMutectCalls0 votes 0 comments
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How to specify number of threads while running Mutect20 votes 0 comments
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Best practice trios0 votes 0 comments
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BuildBamIndex0 votes 4 comments
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Can't access google cloud it says permission required0 votes 2 comments
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RGID versus RGPU0 votes 1 comment
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Picard SortSam error Answered0 votes 3 comments
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Issues with LiftoverVcf Answered0 votes 6 comments
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Documentation for interval files in resource bundle0 votes 1 comment
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UmiAwareMarkDuplicatesWithMateCigar - UMI_METRICS0 votes 2 comments