Documentation Questions
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Difference between GATK Germline CNV Pipeline vs Genome STRiP? Answered0 votes 8 comments
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error-handling-end-exit-codes-in-gatk0 votes 1 comment
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GenomAD files for MuTect2 Answered0 votes 9 comments
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ASEReadCounter count each read only once or not0 votes 1 comment
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Germline CNV vs HaplotypeCaller/indels0 votes 1 comment
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What is the correct step? VQSR and CNNScoreVariants? Answered0 votes 2 comments
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BQSR Spark: Why Beta? Answered0 votes 3 comments
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After SNPs and INDELs are extracted, can they be recombined later? Answered0 votes 1 comment
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Mulitple mapped reads in germline CNV caller (GermlineCNVCaller) Answered0 votes 1 comment
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The base of logarithm for VQSLOD0 votes 1 comment
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Funcotator misses many Cosmic fields - update possible?0 votes 1 comment
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Mutect2 call some structural variants as indel ,how to filter it? Answered0 votes 3 comments
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producing strandedness metrics from rnaseq data Answered0 votes 1 comment
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Picard RnaSeqMetrics CORRECT_STRAND_READS and INCORRECT_STRAND_READS0 votes 1 comment
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Output of PossibleDeNovo Answered0 votes 2 comments
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Questions Regarding VCF Files Found in hg38 Public Resource Bundle0 votes 4 comments
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gCNV2 votes 1 comment
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MergeBamAlignment input files? Answered0 votes 3 comments
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Unix pipe support and SAM fields used in Variant Calling pipeline Answered0 votes 2 comments
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How can I get AF for each sample in GVC JointGenotyping mode? Answered0 votes 3 comments
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HaplotypeCaller vcf file analysis Answered0 votes 2 comments
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Where do I find sample dataset for practice? Answered0 votes 2 comments
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Map reads to a reference with alternate contigs like GRCH38 using GATK40 votes 3 comments
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Create Somatic PON threshold Answered0 votes 1 comment
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GATK-CollectVariantCallingMetrics - regarding more information0 votes 1 comment
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panel of normal hg19 version Answered0 votes 1 comment
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How is AC calculated?0 votes 1 comment
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GATK CNV interpret Segment_Mean and MEAN_LOG2_COPY_RATIO Answered0 votes 3 comments
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What does PCT_MIX from CreateVerifyIDIntensityContaminationMetricsFile mean?0 votes 2 comments