snipar 0.0.5

Library and command line scripts for inferring identity-by-descent (IBD) segments shared between siblings, imputing missing parental genotypes, and for performing family based genome-wide association and polygenic score analyses.

snipar

snipar (single nucleotide imputation of parents) is a python library for inferring identity-by-descent (IBD) segments shared between siblings, imputing missing parental genotypes from observed genotypes and IBD segments in a nuclear family, and for performing family based genome-wide association and polygenic score analyses using observed and/or imputed parental genotypes.

Main features:

Infer identity-by-descent segments shared between siblings (ibd.py).

Impute missing parental genotypes given the observed genotypes in a nuclear family (impute.py).

Perform family based GWAS using observed and imputed parental genotypes (gwas.py).

Compute polygenic scores for probands, siblings, and parents from SNP weights using observed/imputed parental genotypes, and perform family based analysis of polygenic scores (pgs.py script).

Compute genome-wide correlations between different effects estimated by gwas.py (correlate.py).

Documentation

It is recommended to work through the tutorial: https://snipar.readthedocs.io/en/latest/tutorial.html

Virtual Environment

We highly recommend using a python distribution such as Anaconda 3 (https://store.continuum.io/cshop/anaconda/). You may encounter problems with the installation due to package conflicts with your existing Python installation. To overcome this, you can try installing in a virtual environment. In a bash shell, this could be done by using the following commands in your directory of choice:

python -m venv path-to-where-you-want-the-virtual-environment-to-be

You can activate and use the environment using

source path-to-where-you-want-the-virtual-environment-to-be/bin/activate

Installing Using Pip

Just run:

pip install snipar

Sometimes this may not work because the pip in the system is outdated. You can upgrade your pip using:

pip install --upgrade pip

Installing From Source

To install from source, clone the git repository, and in the directory containing the snipar source code, at the shell type:

python setup.py install

Running tests

To check that the code is working properly and that the C modules have been compiled, you should run tests. To run the tests, after the installation run this command:

python -m unittest snipar.tests