biomguler / G-WASPiper

This repository is my collection of pipelines for basic GWAS analysis, written in R to simplify, please cite original tools/approaches referred in the pipelines.

G-WASPiper

Source of photo: DOI Link

G-WASPiper

• 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

• all main function will be added here in text and table!!!

Short description and main usage

What is G-WASPiper?

• 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.

What is NOT G-WASPiper?

• 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.

How frequently it will updated?

• 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.

License for G-WASPiper and other Softwares

• 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.

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

Step-by-step G-WASPiper

• Full documentation is available at the wiki page

Sources

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.

How to cite

• will be updated

Sample Data

• will be updated

Contacts

• Github:
  • https://github.com/biomguler/G-WASPiper/issues
• Email:
  • [e-mail]
  • [e-mail]