Documentation Questions
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MarkDuplicates not checking sequences Answered0 votes 3 comments
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Best practice to deal with spanning deletion for downstream analysis Answered0 votes 3 comments
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Using -"-allow-old-rms-mapping-quality-annotation-data" to force genotyping gvcf created with old version Answered0 votes 1 comment
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GATK VariantEval no concordance between dbSNP and our data Answered0 votes 6 comments
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Theorical model for Active region detection Answered0 votes 6 comments
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BQSR --use-original-qualities0 votes 1 comment
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ASEReadCounter and overlapping paired reads0 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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GATK4 Best Practices -- SetNmMdAndUqTags0 votes 1 comment
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GATK Mutect2 tumor vs. normal sample Answered0 votes 2 comments
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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