Documentation Questions
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Germline CNV vs HaplotypeCaller/indels0 votes 1 comment
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ASEReadCounter count each read only once or not0 votes 1 comment
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error-handling-end-exit-codes-in-gatk0 votes 1 comment
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What do the two different minimum base quality filters do in Mutect2?0 votes 3 comments
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Funcotator misses many Cosmic fields - update possible?0 votes 1 comment
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panel of normal hg19 version Answered0 votes 1 comment
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The base of logarithm for VQSLOD0 votes 1 comment
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GATK-CollectVariantCallingMetrics - regarding more information0 votes 1 comment
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Germline Resouce Answered1 vote 3 comments
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Create Somatic PON threshold Answered0 votes 1 comment
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Map reads to a reference with alternate contigs like GRCH38 using GATK40 votes 3 comments
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Mulitple mapped reads in germline CNV caller (GermlineCNVCaller) Answered0 votes 1 comment
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After SNPs and INDELs are extracted, can they be recombined later? Answered0 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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GATK CNV interpret Segment_Mean and MEAN_LOG2_COPY_RATIO Answered0 votes 3 comments
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gCNV2 votes 1 comment
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Questions Regarding VCF Files Found in hg38 Public Resource Bundle0 votes 4 comments
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Output of PossibleDeNovo Answered0 votes 2 comments
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Picard RnaSeqMetrics CORRECT_STRAND_READS and INCORRECT_STRAND_READS0 votes 1 comment
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How is tumor_f in Funcotator MAF Answered0 votes 3 comments
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CollectAllelicCounts interval_list Answered1 vote 15 comments
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mutect2 multi-sample Answered0 votes 29 comments
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GenomAD files for MuTect2 Answered0 votes 9 comments
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GATK4 Best Practices -- SetNmMdAndUqTags0 votes 1 comment
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ask for target sequencing pipeline code using Mutect2 (gatk 4.1.7.0)0 votes 1 comment
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ASEReadCounter and overlapping paired reads0 votes 1 comment
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BQSR --use-original-qualities0 votes 1 comment