Documentation Questions
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Maximum number of Plasma samples by use mutect2 multi-sample pipeline0 votes 0 comments
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GATK Funcotator MAF header0 votes 0 comments
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Extraction standards for SNP and INDEL0 votes 1 comment
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HaplotypeCaller dont call high supported variant0 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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How to prioritize EGFR transcript for annotation in Funcotator?0 votes 1 comment
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gatk4.3.0.0 Combines gvcfs were interrupted without errors0 votes 2 comments
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Cannot find explanation for odd vcf genotype format0 votes 1 comment
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What argument(s) should be used instead of --debug-graph-transformations?0 votes 3 comments
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How to Split 3000 WGS CRAM files into 1Mbp length chunks0 votes 1 comment
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BOTHSIDES_SUPPORT filter in GATK-SV VCF0 votes 2 comments
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Confusion regarding the Picard EstimateLibraryComplexity utility0 votes 1 comment
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Collecting chrM reads for mitochondrial analysis & MarkDuplicates0 votes 1 comment
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using the PlotDenoisedCopyRatios() function in gatk40 votes 1 comment
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GATK-SV VCF interpretation0 votes 2 comments
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CONVERT BAM TO U-BAM0 votes 1 comment
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Explanation on the HS Penalty metric1 vote 3 comments
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SPLICE_SITE specification in Funcotator0 votes 2 comments
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is --dont-use-soft-clipped-bases discarded in HaplotypeCaller?0 votes 1 comment
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Genotype filtering still write "PASS" in filter field1 vote 7 comments
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Picard CollectHsMetrics PCT_TARGET_BASES Output0 votes 2 comments
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error:Argument --emit-ref-confidence0 votes 0 comments
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Funcotator 4.1.2.0 gencode for locatableXSV0 votes 1 comment
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Intervals and GenomicsDBImport0 votes 2 comments
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How does Mutect2 count read depth/coverage? Answered1 vote 11 comments