Documentation Questions
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Germline sites in Mutect2 Answered0 votes 13 comments
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How does Mutect2 count read depth/coverage? Answered1 vote 11 comments
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CallCopyRatioSegments -- how does it work? Answered0 votes 3 comments
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Why don't I have access to some links? Answered0 votes 3 comments
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GATK Mutect2 tumor vs. normal sample Answered0 votes 4 comments
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vcf files for BQSR step Answered1 vote 4 comments
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mutect2 multi-sample Answered0 votes 35 comments
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Picard SortSam error Answered0 votes 3 comments
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Issues with LiftoverVcf Answered0 votes 6 comments
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SamToFastq - bam order Answered0 votes 6 comments
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HaplotypeCaller using one sample split in two bam files Answered0 votes 3 comments
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ASEReadCount Only Outputting the First Chromosome Answered0 votes 3 comments
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Too many duplicate articles Answered0 votes 2 comments
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Where is the list of annotations and annotation groups? Answered2 votes 7 comments
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germline mutation calling using per-sample module Answered0 votes 2 comments
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ASEReadCounter outputting blank table Answered0 votes 4 comments
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GATK CNV somatic panels of normal design Answered0 votes 3 comments
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Mitochondrial shifted reference Answered0 votes 4 comments
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Limit core use of DetermineGermlineContigPloidy & GermlineCNVCaller Answered1 vote 1 comment
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GATK genomicsDBImport error Answered0 votes 3 comments
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Documentation for running GATK and Cromwell on IBM Cloud Answered1 vote 7 comments
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Haplotypecaller Answered0 votes 1 comment
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JointGermlineCNVSegmentation Answered0 votes 2 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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GetPileupSummaries common germline variant sites VCF hg38 Answered0 votes 2 comments
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MergeBamAlignment for mitochondrial variant discovery Answered0 votes 1 comment
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how to run "gatk-register"? Answered0 votes 2 comments
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MergeBamAlignment conflicting headers between mapped and unmapped Answered0 votes 3 comments