This repository contains tools for performing record matching of STR profiles with fragmentary genomic SNP profiles, as described in Kim and Rosenberg. The record matching pipeline starts with a set of reference files containing SNP-STR genotypes on reference individuals, a set of files containing STR profiles only on test individuals, a set of files containing SNP profiles only on test individuals, and a set of genetic map files. It outputs a match-score matrix for all STR-SNP pairs, with rows indicating STR profiles and columns indicating SNP profiles. It enables hypothesis tests for a variety of relatedness hypotheses based on SNP and STR profiles. For a demonstration of the record matching pipeline, please see Example. The repository also includes scripts to generate simulated pedigrees and fragmentary genomic SNP data.

• BEAGLE 4.1
• Java version 8 - required by BEAGLE. See BEAGLE manual for details.
• VCFtools. conda version is also available here.

• A phased reference SNP-STR haplotype panel of Saini et al. from the 1000 Genomes Project phase 3 containing 2,504 individuals can be downloaded from here. Processed data containing 1-Mb SNP windows extending 500 kb in each direction from each CODIS locus midpoint can be found under data/1KGP.
• HGDP SNP-STR data containing 872 individuals can be downloaded from here.
• Human genetic maps. HapMap GrCh36 and GrCh37 genetic maps in PLINK format. Can be downloaded from BEAGLE page.
• All genotypes in the reference panel must be non-missing and phased for BEAGLE imputation.

Kim J, Rosenberg NA (2022). Record-matching of STR profiles with fragmentary genomic SNP data. bioRxiv, 2022.09.01.505545. 10.1101/2022.09.01.505545.

Kim J, Edge MD, Algee-Hewitt BFB, Li JZ, Rosenberg NA (2018). Statistical detection of relatives typed with disjoint forensic and biomedical loci. Cell, 175(3):848-858.e6. 10.1016/j.cell.2018.09.008.

Edge MD, Algee-Hewitt BFB, Pemberton TJ, Li JA, Rosenberg NA (2017). Linkage disequilibrium matches forensic genetic records to disjoint genomic marker sets. PNAS, 114(22):5671-5676. 10.1073/pnas.1619944114.