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Thanks for your interest in Tractor!

The methodology and utility of Tractor is more fully described in our publication, "Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power", which is was published in Nature Genetics here. We ask that you cite this manuscript for work utilizing the Tractor software.

In this repo, we provide scripts comprising the full Tractor pipeline for (1) recovering long-range haplotypes as informed by local ancestry deconvolution, (2) extracting ancestral segments and calculating ancestral minor allele dosages, and (3) running our local ancestry aware GWAS model.

The pipeline is currently designed assuming RFmix_v2 and phased VCF format genotype input and consists of separate scripts for maximum flexibility of use. These scripts can be run in sequence to do all the steps or, if long-range tracts will not impact the goals of the analysis, the user can skip right to ancestry dosage calculation and running our GWAS model.

Note: The success of Tractor relies on good local ancestry calls. Please ensure your LAI performance is highly accurate before running a Tractor GWAS.

Update (Feb 2022): We have designed a python-based implementation of the Tractor GWAS model for both linear and logistic regression! Please see the sub-page for this 'local' version which may be more accessible across compute environments.