Software to compute and histogram pairwise LD metrics


LDBIRD is a command-line program for computing LD metrics between all pairs of variants in its input files.

In working on the paper described below, I needed a way to quickly assess the distribution of between-chromosome LD in P.falciparum populations - as well as finding individual pairs of variants with outlying LD. Thus LDBIRD was born. The key features LDBIRD has are:

For an introduction to running LDBIRD, please see the getting started page.

How fast is LDBIRD?

LDBIRD is likely not the fastest way you can compute LD. It limits itself to loading variants one (or rather two) at a time, and thus its algorithm is quadratic in the number of variants. If LDBIRD doesn't meet your needs, other ways to compute LD are to use plink or LDStore - or possibly tskit.

Obtaining LDBIRD

LDBIRD is currently included as part of the QCTOOL package, which is currently hosted at code.enkre.net. See the download page for full details on obtaining and installing LDBIRD.


LDBIRD was originally developed for a study of human and malaria parasite variation in samples collected for MalariaGEN Consortial Project 1. If you use LDBIRD in published work, please cite the following preprint (or its published equivalent):

"The protective effect of sickle cell haemoglobin against severe malaria depends on parasite genotype", bioRxiv https://doi.org/10.1101/2021.03.30.437659
Gavin Band, Ellen M. Leffler, Muminatou Jallow, Fatoumatta Sisay-Joof, Carolyne M. Ndila, Alexander W. Macharia, Christina Hubbart, Anna E. Jeffreys, Kate Rowlands, Thuy Nguyen, Sonia M. Goncalves, Cristina V. Ariani, Jim Stalker, Richard D. Pearson, Roberto Amato, Eleanor Drury, Giorgio Sirugo, Umberto d'Alessandro, Kalifa A. Bojang, Kevin Marsh, Norbert N.P. Peshu, David J. Conway, Thomas N. Williams, Kirk A. Rockett, Dominic P. Kwiatkowski


For more information or questions, please contact me at gavin [dot] band (at) well.ox.ac.uk.