Pipeline Index
Best Practices Workflows | Created 2019-07-14 | Last updated 2019-07-14

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This document is under construction. It aims to provide an overview of use cases covered by GATK Best Practices workflows.

Variant Discovery Germline Somatic Notes
Data pre-processing Single-sample Single-sample Same workflow applies to all
Short variants: SNPs and Indels Single-sample & Joint Calling Tumor-Normal & Tumor-Only
Copy Number Variants (CNVs) Multisample Tumor-Normal & Tumor-Only
Structural Variants (SVs) In progress TBD
Special use cases Notes
Metagenomic analysis (PathSeq)
Mitochondrial short variants
Liquid blood biopsy

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