Documentation Questions
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Known Sites for BQSR Answered4 votes 5 comments
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Difference between the different annotation groups available in GATK2 votes 1 comment
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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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Documentation for running GATK and Cromwell on IBM Cloud Answered1 vote 4 comments
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genotyping calls don't align with coverage Answered1 vote 1 comment
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Where is the list of annotations and annotation groups? Answered1 vote 6 comments
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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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BaseRecalibrator --max-cycle Answered0 votes 1 comment
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Question on Java version Answered0 votes 2 comments
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GATK CNV somatic panels of normal design0 votes 2 comments
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JointGermlineCNVSegmentation0 votes 2 comments
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GetPileupSummaries common germline variant sites VCF hg38 Answered0 votes 2 comments
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how to run "gatk-register"? Answered0 votes 2 comments
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MergeBamAlignment for mitochondrial variant discovery Answered0 votes 1 comment
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Single sample germline - VQSR+CNN or just CNN0 votes 5 comments
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Is FilterAlignmentArtifacts out of the Mutect2 calling best practices? Answered0 votes 1 comment
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MergeBamAlignment conflicting headers between mapped and unmapped Answered0 votes 3 comments
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VariantsToTable not working Answered0 votes 2 comments
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Genomes in the cloud docker file0 votes 0 comments
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GATK GenotypeGVCFs miss a real Insertion Answered0 votes 6 comments
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How to evlauate the result: GenotypeConcordance or Concordance Answered0 votes 6 comments
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Mitochondrial shifted reference Answered0 votes 2 comments