MungeSumstats: A Bioconductor package for the standardisation and quality control of many GWAS summary statistics

Abstract

SummaryGenome-wide association studies (GWAS) summary statistics have popularised and accelerated genetic research. However, a lack of standardisation of the file formats used has proven problematic when running secondary analysis tools or performing meta-analysis studies. To address this issue, we have developed MungeSumstats, a Bioconductor R package for the standardisation and quality control of GWAS summary statistics. MungeSumstats can handle the most common summary statistic formats, including variant call format (VCF) producing a reformatted, standardised, tabular summary statistic file, VCF or R native data object. ContactAlan Murphy: a.murphy@imperial.ac.uk, Nathan Skene: n.skene@imperial.ac.uk Availability and implementationMungeSumstats is available on Bioconductor (v 3.13) and can also be found on Github at: https://neurogenomics.github.io/MungeSumstats Supplementary informationThe analysis deriving the most common summary statistic formats is available at: https://al-murphy.github.io/SumstatFormats