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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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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Select Variants0 votes 2 comments
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GATK problem with the CombineGVCFs0 votes 1 comment
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How to use the --alleles option of HaplotypeCaller ?0 votes 8 comments
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Picard MarkDuplicates Functionality0 votes 1 comment
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Missing documentation on somatic variant calling output VCF0 votes 1 comment
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MergeMutectStats missing from documentation0 votes 1 comment
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What is the recommended way to use/parse Funcotator output?0 votes 1 comment
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Maximum number of Plasma samples by use mutect2 multi-sample pipeline0 votes 2 comments
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GATK Funcotator MAF header0 votes 1 comment