Recombination maps generated using pyrho for autosomes and X chromosomes from the Thousand Genomes Project (1KGP), realigned to the T2T-CHM13 reference genome v2.0.
Data is available here and at https://zenodo.org/records/14891074
Specifically, this directory contains three types of data:
Masked: Recombination maps created after application of a short read accessibility mask, removing regions with low-confidence read alignment.No mask: Recombination maps created without use of an accessibility mask.No mask, scaled to deCODE: Recombination maps created without use of an accessibility mask and subsequently scaled to deCODE map lengths.
Each set of recombination maps is available as a set of population-specific maps and as an averaged map for the entire 1KGP dataset.
Each directory contains more a specific README
Contains all non-vcf files necessary for running scripts.
All scripts used for generating recombination maps. Contains scripts for the following:
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preprocessing: Necessary scripts to run on 1KGP vcfs prior to creating recombination maps. Separates vcfs per population and applies quality filtering to chrX vcfs. -
autosomes: Directory contains scripts to create per-population and averaged recombination maps for all autosomes. -
chrX: Contains scripts to apply accessibility mask to chrX and separate per population. Contains directories with recombination map scripts for pseudoautosomal and non-pseudoautosomal regions -
variance_sorted_1mb.csv- table of variance in recombination rates across populations. Sorted in descending order. Variance was computed in nonoverlapping 1 Mb windows.