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.
Project description
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Sometimes this may not work because the pip in the system is outdated.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
Project details
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