score
score is a free software tool suite released under the MIT license for working with GWAS-VCF summary statistics files
the score software tool suite is entirely written in C as a set of BCFtools plugin. It can be compiled with BCFtools or downloaded as a set of binary files. It requires BCFtools 1.19 or newer to run. A script to plot summary statistics is also provided based on ggplot2
Download
You can download from this page the latest Linux x86_64 BCFtools
plugin binaries for
the stable version and
the development version
Source code is also available for the the stable version and the development version
To run a BCFtools plugin binary, say score.so, there are four options:
$ export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins && bcftools +score
$ export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins && bcftools plugin score
$ bcftools +$BCFTOOLS_PLUGINS/score.so
$ bcftools plugin $BCFTOOLS_PLUGINS/score.so
We also provide the the LDGM-VCF matrices to run BCFtools/blup and BCFtools/pgs:
ldgms.GRCh38.zip - LDGM-VCF precision matrix files (approx. 3GB) updated on 2022-11-29
To find more information on how to run the software, try our github page. For any feedback, send an email to giulio.genovese@gmail.com
Beta
For Ubuntu users, a debian package will be provided in the future to install the plugins
Publications
Publications that used score (or munge, liftover, metal, blup, or pgs):
2024
- Francis, M. et al. Multi-ancestry genome-wide association meta-analysis of mosaic loss of chromosome Y in the Million Veteran Program identifies 167 novel loci. medRxiv (2024) doi:10.1101/2024.04.24.24306301
- Purdue, M. P. et al. Multi-ancestry genome-wide association study of kidney cancer identifies 63 susceptibility regions. Nature Genetics (2024) doi:10.1038/s41588-024-01725-7
- Genovese, G. et al. BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies. Bioinformatics (2024) doi:10.1093/bioinformatics/btae038
- Ling, E. et al. Concerted neuron-astrocyte gene expression declines in aging and schizophrenia. bioRxiv (2024) doi:10.1101/2024.01.07.574148
2023
- Gupta, R. et al. Nuclear genetic control of mtDNA copy number and heteroplasmy in humans. Nature (2023) doi:10.1038/s41586-023-06426-5
- Peachey, N. et al. Multi-ancestry GWAS of Fuchs corneal dystrophy highlights roles of laminins, collagen, and endothelial cell regulation. Research Square (2023) doi:10.21203/rs.3.rs-2762003/v1
Releases
Version development source and Linux x86_64 binaries (compiled for BCFtools 1.19)
Version 2023-09-19 source and Linux x86_64 binaries (compiled for BCFtools 1.17, includes a regression for BCFtools/liftover)
Version 2022-12-21 source and Linux x86_64 binaries (compiled for BCFtools 1.16)
Credits
score is developed by Giulio Genovese at the Broad Institute and at the McCarroll Lab in the Harvard Medical School Department of Genetics under the supervision of Steven McCarroll
We would like to thank the following people: Luke O'Connor at the Broad Institute for advice with the implementation of BLUPx, Bryan Gorman at the VA for feedback and testing with the score pluing, Heng Li, Petr Danecek, John Marshall, James Bonfield, and Shane McCarthy for developing HTSlib and BCFtools