Best Practices Workflows
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Getting started with GATK4
GATK, pronounced "Gee Ay Tee Kay" (not "Gat-Kay"), stands for GenomeAnalysisT... -
Germline copy number variant discovery (CNVs)
Purpose Identify germline copy number variants. Diagram is not available ... -
Pipeline Index
This document is under construction. It aims to provide an overview of use ca... -
Somatic short variant discovery (SNVs + Indels)
Purpose Identify somatic short variants (SNVs and Indels) in one or more tum... -
Germline short variant discovery (SNPs + Indels)
Important: This document is currently being updated Purpose Identify germ... -
Data pre-processing for variant discovery
Purpose The is the obligatory first phase that must precede all variant disc... -
Somatic copy number variant discovery (CNVs)
Purpose Identify somatic copy number variant (CNVs) in a case sample. Requir... -
About the GATK Best Practices
This document provides important context information about how the GATK Best ... -
RNAseq short variant discovery (SNPs + Indels)
Purpose Identify short variants (SNPs and Indels) in RNAseq data. Ref...