Documentation Questions
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gatk FilterByOrientationBias Answered0 votes 2 comments
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GenomicsDBImport java error0 votes 1 comment
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GATK VariantEval no concordance between dbSNP and our data Answered0 votes 6 comments
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What does mutect2 do if two bams are input and --normal-sample is not specified? Answered0 votes 1 comment
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ApplyBQSRSpark ApplyBQSR has different results0 votes 3 comments
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GC DROPOUT AND AT DROPOUT Answered0 votes 1 comment
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Determining Optimal Number of Samples to include in Panel of Normal Answered0 votes 2 comments
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every exon junctions in Bam files got softclipped after run SplitNCigarReads Answered0 votes 4 comments
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How does Picard basecalling make decisions on NovaSeq data? Answered0 votes 4 comments
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GATK 4.2.0.0 Haplotype caller --genotyping_mode DISCOVERY Option Answered0 votes 2 comments
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Error remove 0x1 from alternate contigs tutorial Answered0 votes 5 comments
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CreateSomaticPanelOfNormals BETA tag Answered0 votes 2 comments
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Sensitivity analysis for GATK CNV PoN Answered0 votes 1 comment
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Mutect2 merge stats Answered0 votes 2 comments
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Error HaplotypeCaller from alternate contigs tutorial Answered0 votes 4 comments
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BedToIntervalList and IntervalListTools: can interval lists without unique names for intervals be used? Answered0 votes 4 comments
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Germline sites in Mutect2 Answered0 votes 11 comments
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Potential updates to GATK HaplotypeCaller documentation0 votes 1 comment
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Alt Contig tutorial question Answered0 votes 7 comments
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Three questions about calling CNV in Germline. Answered0 votes 7 comments
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Mutect2 panel of normals design Answered0 votes 2 comments
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Truth set download page for BQSR Answered0 votes 2 comments
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Converting Reference Genomes from b37 to hg190 votes 4 comments
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Known Sites for BQSR Answered5 votes 5 comments
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RADseq/MIGseq denovo SNP calling in tetraploid plants Answered0 votes 3 comments
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HaplotypeCaller vcf file analysis Answered0 votes 2 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