ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.
This repository is a (manual copy) fork of a (github) for of the repos https://github.com/bulik/ldsc. See here the list of fork of the original https://github.com/bulik/ldsc/forks.
The originating fork of this repository fixed major issues regarding Python2 Python3 port as well as some pandas oldies. Unfortunately the originating fork is unknown.
This repos was reorganized to fit the standards of Python package generation and advanced standard to be handle by package generators like rattler. The main consequences are the apparition of the Pyproject.toml and the move of scripts file into the ldscore directory.
You can download European and East Asian LD Scores from 1000 Genomes here. These LD Scores are suitable for basic LD Score analyses (the LD Score regression intercept, heritability, genetic correlation, cross-sex genetic correlation). You can download partitioned LD Scores for partitioned heritability estimation here.
Before contacting us, please try the following:
- The wiki has tutorials on estimating LD Score, heritability, genetic correlation and the LD Score regression intercept and partitioned heritability.
- Common issues are described in the FAQ
- The methods are described in the papers (citations below)
If that doesn't work, you can get in touch with us via the google group.
Issues with LD Hub? Email [email protected]
If you use the software or the LD Score regression intercept, please cite
For genetic correlation, please also cite
- Bulik-Sullivan, B., et al. An Atlas of Genetic Correlations across Human Diseases and Traits. Nature Genetics, 2015. Preprint available on bioRxiv doi: http://dx.doi.org/10.1101/014498
For partitioned heritability, please also cite
- Finucane, HK, et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nature Genetics, 2015. Preprint available on bioRxiv doi: http://dx.doi.org/10.1101/014241
For stratified heritability using continuous annotation, please also cite
If you find the fact that LD Score regression approximates HE regression to be conceptually useful, please cite
Bulik-Sullivan, Brendan. Relationship between LD Score and Haseman-Elston, bioRxiv doi: http://dx.doi.org/10.1101/018283
For LD Hub, please cite
This project is licensed under GNU GPL v3.
Brendan Bulik-Sullivan (Broad Institute of MIT and Harvard)
Hilary Finucane (MIT Department of Mathematics)