Documentation Questions
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Why don't I have access to some links? 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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"NotDuplicateReadFilter" behaviour in HaplotypeCaller Answered0 votes 3 comments
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What's wrong with my GATK HaplotypeCaller step's codes?0 votes 1 comment
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How can I get Sample Summary0 votes 1 comment
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Append GenomicsDBimport Answered0 votes 3 comments
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GATK4.2.3.0 HaplotypeCaller error0 votes 1 comment
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picard sortvcf: what does it do? Answered0 votes 7 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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FilterFuncotations Duplicate key error Answered0 votes 7 comments
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haplotypeCaller phasing Answered0 votes 11 comments
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Difference between the different annotation groups available in GATK2 votes 1 comment
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use LearnReadOrientationModel to build artifact-prior.tar.gz Answered0 votes 5 comments
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Mark duplicates in merged bam files sorted by coordinates0 votes 2 comments
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How do I call somatic mitochondrial variants? Answered0 votes 3 comments
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`FilterMutectCalls` for normal only calls Answered0 votes 4 comments
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countsN meaning & example Answered0 votes 2 comments
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GATK VariantFiltration Error Answered0 votes 3 comments
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SelectVariants --discordance not working as I expected Answered0 votes 3 comments
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Interpretation of gene_summary output from DepthofCoverage Answered0 votes 11 comments
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GenotypeGVCFs only accepts single combinedGVCF? CombineGVCFs & genomicsdb errors... .interval_list subset Answered0 votes 12 comments
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Where do I find resources for using FilterVariantTranches with CNN_2D/CNN_1D scores? Answered0 votes 1 comment
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Does CollectReadCounts Count Fragments or Individual Reads? Answered0 votes 3 comments
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MarkDuplicates not checking sequences Answered0 votes 3 comments
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Where is the list of annotations and annotation groups? Answered1 vote 6 comments