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 |
2 comments
good!
It is better to add the links for each step in the table. thanks.
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