ersa estimates the combined number of generations between pairs of individuals using a Germline matchfile as input. It is an implementation of Huff et. al. (2011) Maximum-Likelihood estimation of recent shared ancenstry (ERSA) and Li et. al. (2014) Relationship Estimation from Whole-Genome Sequence Data.

Copyright (c) 2015 by

• Richard Muñoz ([email protected])
• Jie Yuan ([email protected])
• Yaniv Erlich ([email protected])

License: GNU GPL v3 (see LICENSE.txt)

ersa requires Python 3.4 or greater. In addition, the following packages for python3 must be installed prior to the installation process:

• numpy
• setuptools

First, install python3, setuptools, and numpy. Then clone from github:

git clone https://github.com/rmunoz12/ersa.git
cd ersa
sudo python3 setup.py install

This will add ersa to your path and download additional required python packages.

Requires a Germline matchfile as input. By default, summary results are sent to stdout, but can also be directed to a file. Alternatively, full results can be directed to a database, as in the example below.

$ ersa -D "sqlite:///ersa_results.db" input.match

This creates ersa_results.db in current directory.

For additional options, use

$ ersa -h

On inserting results into a database, if a comparison between a pair of individuals exists, ersa will mark the old result as deleted (i.e., soft delete the result). To physically delete these old results from the database, a utlity ersa_delete_rows is also provided:

$ ersa_delete_rows "sqlite:///ersa_results.db"