IBDGem-LRs

This repository contains code used for the study "On forensic likelihood ratios from low-coverage sequencing." It is structured as follows:

1. Scripts

This directory contains all the scripts used to simulate the different scenarios mentioned in our paper.

• Diploid LD: Contains scripts for simulating complete and perfect linkage disequilibrium scenarios in the diploid setting investigated in the paper.
• Diploid no LD: Contains scripts for simulating diploid genotypes derived under neutral, CEU, or YRI site frequency spectra (SFS).
• Fraction of Unique Genotypes: Contains scripts for working with the 1kGP VCF file to obtain results shown in Figure S5.
• Haploid: Contains scripts for simulating haploid genotypes and running both complete and perfect LD scenarios.
• IBDGem Bash Scripts: Contains the scripts used to run IBDGem on the simulated data.
• Recommendations: Contains scripts for simulating scenarios in which IBDGem produces approximately correct outputs.
• Robustness to Phase: Contains scripts to simulate two scenarios:
  1. Shuffled haplotypes in the reference panel.
  2. Inclusion of the target individual's haplotypes in the reference panel in either the same individual or across two different individuals.

2. Unique genotype stats

This directory contains the fractions of unique genotypes across the 100 different starting locations on chromosome 1, generated with different settings.

3. 1kGP SFS

This directory contains output from the 1kGP analysis, including allele frequency distributions for each of the CEU and YRI subpopulations.