G-WASPiper

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.

Main Functions and Scripts

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-WASPiper is 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-WASPiper in your works please look How to cite section below.

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.