Documentation Questions
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Known Sites for BQSR Answered5 votes 5 comments
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How does Mutect2 count read depth/coverage? Answered2 votes 11 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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Issues with LiftoverVcf GRch37 to GRch381 vote 6 comments
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FilterMutectCalls: Missing documentation for --mitochondria-mode1 vote 2 comments
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HOW TO EXCLUDE FILTERED VARIANTS WITH VARIANTFILTRATION?1 vote 1 comment
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License / use terms for GATK resource bundle1 vote 2 comments
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Explanation on the HS Penalty metric1 vote 3 comments
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Genotype filtering still write "PASS" in filter field1 vote 7 comments
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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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Funcotator to search in NCBI rather than Ensemble Database0 votes 1 comment
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Using Illumina Masked References with BWA MEM0 votes 2 comments
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VariantRecalibrator Error about Argument 'resource' was missing0 votes 1 comment
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JointGermlineCNVSegmentation (BETA)0 votes 2 comments
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Somatic Calling with Mutect20 votes 1 comment
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Broken GATK4 documentation links0 votes 4 comments