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https://github.com/Al-Murphy/MungeSumstats
Rapid standardisation and quality control of GWAS or QTL summary statistics
https://github.com/Al-Murphy/MungeSumstats
bioconductor-package bioinformatics database-api genomics gwas qtl r r-package standardisation summary-statistics vcf-files
Last synced: 19 days ago
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Rapid standardisation and quality control of GWAS or QTL summary statistics
- Host: GitHub
- URL: https://github.com/Al-Murphy/MungeSumstats
- Owner: Al-Murphy
- Created: 2021-03-30T08:49:37.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2024-10-30T08:34:15.000Z (about 2 months ago)
- Last Synced: 2024-10-30T09:22:23.167Z (about 2 months ago)
- Topics: bioconductor-package, bioinformatics, database-api, genomics, gwas, qtl, r, r-package, standardisation, summary-statistics, vcf-files
- Language: R
- Homepage: https://doi.org/doi:10.18129/B9.bioc.MungeSumstats
- Size: 8.98 MB
- Stars: 75
- Watchers: 4
- Forks: 15
- Open Issues: 13
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
Awesome Lists containing this project
- awesome-complex-trait-genetics - MungeSumstats
README
---
title: "`MungeSumstats`: Standardise the format of GWAS summary statistics"
author: "
Authors: Alan Murphy, Brian Schilder and Nathan Skene
"
date: "
Updated: `r format(Sys.Date(), '%b-%d-%Y')`
"
bibliography: vignettes/MungeSumstats.bib
csl: vignettes/nature.csl
output: rmarkdown::github_document
vignette: >
%\VignetteIndexEntry{MungeSumstats}
%\VignetteEngine{knitr::rmarkdown}
%\usepackage[utf8]{inputenc}
---
```{r, echo=FALSE}
knitr::opts_chunk$set(tidy = FALSE,
warning = FALSE,
message = FALSE)
```
`r badger::badge_bioc_release(color = "black")`
`r badger::badge_github_version(color = "black")`
`r badger::badge_last_commit(branch = "master")`
`r badger::badge_bioc_download(by = "total", color = "blue")`
`r badger::badge_license()`
`r badger::badge_doi(doi = "https://doi.org/10.1093/bioinformatics/btab665", color="blue")`
# Introduction
The `MungeSumstats` package is designed to facilitate the standardisation of GWAS summary statistics.
## Overview
The package is designed to handle the lack of standardisation of output files by the GWAS community. The [MRC IEU Open GWAS](https://gwas.mrcieu.ac.uk/) team have
provided full summary statistics for >10k GWAS, which are API-accessible via the [`ieugwasr`](https://mrcieu.github.io/ieugwasr/) and [`gwasvcf`](https://github.com/MRCIEU/gwasvcf) packages. But these GWAS are only standardised in the sense that they are VCF format, and can be
fully standardised with `MungeSumstats`.
`MungeSumstats` provides a framework to standardise the format for any GWAS summary statistics, including those in VCF format, enabling downstream integration and analysis. It addresses the most common discrepancies across summary statistic files, and offers a range of adjustable Quality Control (QC) steps.
## Citation
If you use `MungeSumstats`, please cite the original authors of the GWAS
as well as:
> Alan E Murphy, Brian M Schilder, Nathan G Skene (2021)
MungeSumstats: A Bioconductor package for the
standardisation and quality control of many GWAS summary
statistics.
*Bioinformatics*, btab665, https://doi.org/10.1093/bioinformatics/btab665
# Installing `MungeSumstats`
`MungeSumstats` is available on
[Bioconductor](https://bioconductor.org/packages/MungeSumstats).
To install `MungeSumstats` on Bioconductor run:
```R
if (!require("BiocManager")) install.packages("BiocManager")
BiocManager::install("MungeSumstats")
```
You can then load the package and data package:
```R
library(MungeSumstats)
```
Note that there is also a
[docker image for MungeSumstats](https://hub.docker.com/r/neurogenomicslab/mungesumstats).
Note that for a number of the checks implored by `MungeSumstats` a reference
genome is used. If your GWAS summary statistics file of interest relates to
*GRCh38*, you will need to install `SNPlocs.Hsapiens.dbSNP155.GRCh38` and
`BSgenome.Hsapiens.NCBI.GRCh38` from Bioconductor as follows:
```R
BiocManager::install("SNPlocs.Hsapiens.dbSNP155.GRCh38")
BiocManager::install("BSgenome.Hsapiens.NCBI.GRCh38")
```
If your GWAS summary statistics file of interest relates to *GRCh37*, you will
need to install `SNPlocs.Hsapiens.dbSNP155.GRCh37` and
`BSgenome.Hsapiens.1000genomes.hs37d5` from Bioconductor as follows:
```R
BiocManager::install("SNPlocs.Hsapiens.dbSNP155.GRCh37")
BiocManager::install("BSgenome.Hsapiens.1000genomes.hs37d5")
```
These may take some time to install and are not included in the package as some
users may only need one of *GRCh37*/*GRCh38*. If you are unsure of the genome
build, MungeSumstats can also infer this information from your data.
# Getting started
See the [Getting started vignette website](https://al-murphy.github.io/MungeSumstats/articles/MungeSumstats.html)
for up-to-date instructions on usage.
See the [OpenGWAS vignette website](https://al-murphy.github.io/MungeSumstats/articles/OpenGWAS.html)
for information on how to use MungeSumstats to access, standardise and perform
quality control on GWAS Summary Statistics from the MRC IEU [Open GWAS Project](https://gwas.mrcieu.ac.uk/).
Please read carefully through the [FAQ website](https://github.com/Al-Murphy/MungeSumstats/wiki/FAQ)
for an queries about running MungeSumstats. If you have any outside of this
problems please do file an [Issue](https://github.com/al-murphy/MungeSumstats/issues)
here on GitHub.
# Future Enhancements
The `MungeSumstats` package aims to be able to handle the most common
summary statistic file formats including VCF. If your file can not be
formatted by `MungeSumstats` feel free to report the [Issue](https://github.com/al-murphy/MungeSumstats/issues)
on GitHub along with your summary statistics file header.
We also encourage people to edit the code to resolve their particular issues
too and are happy to incorporate these through pull requests on github. If your
summary statistic file headers are not recognised by `MungeSumstats` but
correspond to one of
```
SNP, BP, CHR, A1, A2, P, Z, OR, BETA, LOG_ODDS, SIGNED_SUMSTAT, N, N_CAS, N_CON,
NSTUDY, INFO or FRQ,
```
Feel free to update the `data("sumstatsColHeaders")` following the
approach in the *data.R* file and add your mapping. Then use a [Pull Request](https://github.com/al-murphy/MungeSumstats/pulls) on
GitHub and we will incorporate this change into the package.
# Contributors
We would like to acknowledge all those who have contributed to `MungeSumstats`
development:
* [Alan Murphy](https://github.com/Al-Murphy)
* [Nathan Skene](https://github.com/NathanSkene)
* [Brian Schilder](https://github.com/bschilder)
* [Shea Andrews](https://github.com/sjfandrews)
* [Jonathan Griffiths](https://github.com/jonathangriffiths)
* [Kitty Murphy](https://github.com/KittyMurphy)
* [Mykhaylo Malakhov](https://github.com/MykMal)
* [Alasdair Warwick](https://github.com/rmgpanw)
* [Ao Lu](https://github.com/leoarrow1)