Learn about health, family, and ancestry from human microarray genotyping chip data.
To run the modules, you need some sample genotype data. Currently only 23andMe format data is supported. The file may be uncompressed or gzipped. It would be pretty easy to add support for Ancestry.com or Family Tree DNA downloads.
Sample public 23andMe-format genotypes may be obtained at
OpenSNP. Run make to download three
relevant example genotype files from OpenSNP (~70Mb). Depends on
curl.
Currently there are three programs available, that demonstrate the basics of analyses that can be performed on genotype data.
Example run, with genotype file named datafile
> python estimate_celiac_risk.py datafile
Looks up four markers reported to be associated with Celiac disease, shows the odds ratio associated with each marker, and gives a combined estimate of risk for Celiac disease. Uses values (adjusted odds ratios, prevalence) obtained from 23andMe's Celiac report in October 2014.
Example run, with two genotype files named datafile1 and datafile2
> python assess_relatedness.py datafile1 datafile2
Prints an ASCII-art representation of genetic sharing along chromosome
- Unrelated people will show no sharing; related people will show some or complete sharing depending on the nature of the relationship.
Example run, with genotype file named datafile
> python infer_european_origin.py datafile EUROSNP.genomeorder.frequencies.txt
Evaluates the likelihoods of all six possible pairs of parents, where the source populations are North West Europe, South East Europe, and Ashkenazi Jewish. Meaning, it classifies the supplied genome according to its ancestry, assuming that those are the only possible populations.
Relies on the EUROSNP allele frequencies dataset from Price et al (2008).