Identifying Personal Genomes by Surname Inference
Melissa Gymrek, Amy L. McGuire, David Golan, Eran Halperin, Yaniv Erlich
Science 18 January 2013:
Vol. 339 no. 6117 pp. 321-324
DOI: 10.1126/science.1229566
For a significant percentage of the male population, your Y chromosome together with genealogical databases pretty much give out your last name. This is an attempt at implementing the original attack of Gymrek et al. (or rather reuse the output of their software lobSTR).
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This is an effort to teach myself some computational biology and associated data wrangling. I am neither a biologist nor a computational biologist. I know some of the markers are off, and have not gone through the complete validation tests described in the original paper. Any comment/correction/suggestion welcomed.
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Main file: analyse_str.py (see doc there)
File internet_archive_www_smgf_org_slash_ychromosome_slash_marker_standards.jspx
is an Internet Archive scrape of old website listing correspondance between genealogical and NIST Y-STR markers, located here
Science_Gymrek_et_al/ contains Science original paper and supplementary material
lobSTR_ystr_hg19.bed is a .bed reference file for Y-STRs
1000genomes_20130606_g1k.ped and 1000genomes_20130606_g1k_CEU.ped are pedigree files for 1000 genomes participants
Requires 1000Genomes_Phase_1.vcf file obtained from Gymrek's website