README.md

ancestry-from-panel

Ancestry identification from panel sequencing data using off-target reads

Requirements

• Samtools
• LASER
• BEAGLE
• RFMIX (https://github.com/slowkoni/rfmix)

Usage

Run LASER for ancestry identification.

A BED file of 1000 genome SNP sites and a list of BAM files with full path are required.

sh ancestry_from_panel.sh SNP_sites.bed Bamfiles_list.txt output_prefix

• HGDP.extract.site for LASER is provided in reference folder. Please prepare the HGDP.extract.geno file with SNPs matching the .site file.

Run local ancestry identification.

Please prepare a BED file of selected SNPs to assign ancestry for.

sh offtarget_local_ancestry.sh Bamfiles_list.txt output_prefix

• BEAGLE reference vcf : http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/
• BEAGLE reference map : http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/

Run local ancestry risk score.

This is a simple python script that is an example of how I calculated the cross-validated local ancstry risk score. (k=10 for ten-fold cross-validation)

python local_ancestry_risk_score_kfold.py k