Documentation Questions
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Limit core use of DetermineGermlineContigPloidy & GermlineCNVCaller1 vote 0 comments
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HaplotypeCaller using one sample split in two bam files0 votes 1 comment
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GATK genomicsDBImport error Answered0 votes 3 comments
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germline mutation calling using per-sample module0 votes 1 comment
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Haplotypecaller Answered0 votes 1 comment
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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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GATK CNV somatic panels of normal design Answered0 votes 2 comments
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JointGermlineCNVSegmentation Answered0 votes 2 comments
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GetPileupSummaries common germline variant sites VCF hg38 Answered0 votes 2 comments
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Documentation for running GATK and Cromwell on IBM Cloud Answered1 vote 7 comments
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how to run "gatk-register"? Answered0 votes 2 comments
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MergeBamAlignment for mitochondrial variant discovery Answered0 votes 1 comment
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Single sample germline - VQSR+CNN or just CNN0 votes 5 comments
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genotyping calls don't align with coverage Answered1 vote 1 comment
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Is FilterAlignmentArtifacts out of the Mutect2 calling best practices? Answered0 votes 1 comment
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MergeBamAlignment conflicting headers between mapped and unmapped Answered0 votes 3 comments
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VariantsToTable not working Answered0 votes 2 comments
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Genomes in the cloud docker file0 votes 0 comments
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GATK GenotypeGVCFs miss a real Insertion Answered0 votes 6 comments
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How to evlauate the result: GenotypeConcordance or Concordance Answered0 votes 6 comments
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Mitochondrial shifted reference Answered0 votes 2 comments
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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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Mosaic gCNVs with GATK Answered0 votes 1 comment
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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