Documentation Questions
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Calling somatic CNVs Answered0 votes 6 comments
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GenotypeGVCFs only accepts single combinedGVCF? CombineGVCFs & genomicsdb errors... .interval_list subset Answered0 votes 12 comments
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Where do I find resources for using FilterVariantTranches with CNN_2D/CNN_1D scores? Answered0 votes 1 comment
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Known Sites for BQSR Answered5 votes 5 comments
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CollectAllelicCounts interval_list Answered1 vote 15 comments
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Truth set download page for BQSR Answered0 votes 2 comments
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RADseq/MIGseq denovo SNP calling in tetraploid plants Answered0 votes 3 comments
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Does CollectReadCounts Count Fragments or Individual Reads? Answered0 votes 3 comments
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every exon junctions in Bam files got softclipped after run SplitNCigarReads Answered0 votes 4 comments
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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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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