Documentation Questions
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GATK GenotypeGVCFs miss a real Insertion Answered0 votes 6 comments
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germline-resource Answered0 votes 10 comments
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Mosaic gCNVs with GATK Answered0 votes 1 comment
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WDL pipeline: Mitochondrial-short-variant-discovery Answered0 votes 2 comments
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GenomicsDBImport -L [string] (but for the whole genome): purpose to generate invariant sites Answered0 votes 8 comments
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stand_call_conf and stand_emit_conf in GATK 4.2.4.1 Answered0 votes 1 comment
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"main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit Answered0 votes 4 comments
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CollectReadCounts tutorial incorrectly states default read quality threshold Answered0 votes 1 comment
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Ploidy as an argument in Mutect2 Answered0 votes 5 comments
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"NotDuplicateReadFilter" behaviour in HaplotypeCaller Answered0 votes 3 comments
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picard sortvcf: what does it do? Answered0 votes 7 comments
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What's wrong with my GATK HaplotypeCaller step's codes?0 votes 1 comment
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Append GenomicsDBimport Answered0 votes 3 comments
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How can I get Sample Summary0 votes 1 comment
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GATK Best Practices Mitochondrial Analysis Answered1 vote 45 comments
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GATK4.2.3.0 HaplotypeCaller error0 votes 1 comment
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FilterFuncotations Duplicate key error Answered0 votes 7 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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--dbsnp option in HaplotypeCaller and other programs Answered0 votes 3 comments
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haplotypeCaller phasing Answered0 votes 11 comments
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`FilterMutectCalls` for normal only calls Answered0 votes 4 comments
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How does Genomicsdbimport for polyploids work?0 votes 2 comments
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VariantsToTable GT not extracting correctly Answered0 votes 1 comment
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Difference between the different annotation groups available in GATK2 votes 1 comment
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GATK VariantFiltration Error Answered0 votes 3 comments
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use LearnReadOrientationModel to build artifact-prior.tar.gz Answered0 votes 5 comments
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How do I call somatic mitochondrial variants? Answered0 votes 3 comments
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Interpretation of gene_summary output from DepthofCoverage Answered0 votes 11 comments