GARCOM: A user-friendly R package for genetic mutation counts [version 2; peer review: 2 approved, 1 approved with reservations]
Next-generation sequencing (NGS) has enabled analysis of rare and uncommon variants in large study cohorts. A common strategy to overcome these low frequencies and/or small effect sizes relies on collapsing strategies, i.e. to bin variants within genes/regions. Several tools are now available for ad...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
F1000 Research Ltd
2024-05-01
|
| Series: | F1000Research |
| Subjects: | |
| Online Access: | https://f1000research.com/articles/10-524/v2 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Summary: | Next-generation sequencing (NGS) has enabled analysis of rare and uncommon variants in large study cohorts. A common strategy to overcome these low frequencies and/or small effect sizes relies on collapsing strategies, i.e. to bin variants within genes/regions. Several tools are now available for advanced statistical analyses; however, tools to perform basic tasks such as obtaining allelic counts within defined gene/region boundaries are unavailable or require complex coding. GARCOM (“Gene And Region Count Of Mutations”) library, an open-source freely available package in R language, returns a matrix with allelic counts within genes/regions per sample. GARCOM accepts input data in PLINK or VCF formats, with additional options to subset data for refined analyses. |
|---|---|
| ISSN: | 2046-1402 |