Source of photo: DOI Link
- A handy pipeline for GWAS/genotyping data analysis.
- It can be easly used without having coding skills.
- Each pipelines are general indipentent , and can be highly modified by changing
R scripts.
- all main function will be added here in text and table!!!
- This repository is my collection of pipelines written in R to simplify, please cite original tools/approaches referred in the pipelines. The main idea here is putting every step in a pipe to ensure repredociblity and simplyfy all process.
- The pipeline designed to start from raw genotyping results to create QCed Genotype Data / Ancestery inference / GWAS / TWAS / PRS / MR / xQTL / GWIS / FINE mapping / and many more (will be updated) analysis.
- The main idea here creating standart pipeline for all process by using different approaches/packages/softwares.
- It is my personal reposotry to keep track all pipeline that I am using.
- Of course anyone can used as it or with modifaction.
- I will acknowledge any resourse/pipeline/code inclueded this codes.
- It is not automatic pipeline or click and run pipeline!
- It is not software / package / container. I know there are some R packages or nextflow version that similar with G-WASPiper. But, here idea is creating more flexible and modifiable pipeline that you have control at each step.
- You need to modify some arguments (MAF, INFO, HWE, p value etc.) in the codes, so please be carefull before running any pipeline.
- Some steps and pipelines are need strong computational resources and running this process with out any paralellization/optimization will cost you a lot of time.
- If you have access to any HPC, please run this analysis in side to HPC. The pipelines not optimazated for parallel work.
- It is not a novel package/software, published work. I will try to answer/fix any question/bug, but it would be regulary basic.
- The pipelines will backed-up for each major update. So, anyone can access previous versions.
- Update doesn`t mean changing everything or every pipeline, it usually will be adding more method/script.
- The major updates/adding features will be recorded at the wiki page
- Frequency of the updates will be related request/issue number and personal time.
G-WASPiperis distributed under an MIT license. So, it means you can do nearly everything with this pipelines.- But, please cite the orginal works/software when you use any pipeline depents on the software/package below.
- If you used
G-WASPiperin your works please lookHow to citesection below.
| Software | Link | PMID |
|---|---|---|
| Plink1.9 | Link to Tool A | Publication A |
| Plink2.0 | Link to Tool B | Publication B |
| vcftools/0.1.16 | Link to Tool C | Publication C |
| htslib/1.8 | Link to Tool C | Publication C |
| bcftools/1.9 | Link to Tool C | Publication C |
| anaconda3/2021.05 | Link to Tool C | Publication C |
| fraposa | Link to Tool C | Publication C |
| tidyverse (R) | Link to Tool C | Publication C |
- Full documentation is available at the wiki page
Some of the pipelines modified from:
- Marees, A. T., de Kluiver, H., Stringer, S., Vorspan, F., Curis, E., Marie‐Claire, C., & Derks, E. M. (2018). A tutorial on conducting genome‐wide association studies: Quality control and statistical analysis. International journal of methods in psychiatric research, 27(2), e1608.
- will be updated
- will be updated