mframpton / seqfam

A package primarily designed for analysing next generation sequencing DNA data from families with pedigree information in order to identify rare variants that are potentially causal of a disease/trait.

Seqfam

Documentation is at http://seqfam.readthedocs.io/en/latest/ .

Requirements

Seqfam is compatible with Windows, Mac OS X and Linux operating systems. It is coded using Python 3.6 but can also be run by Python 2.7. It requires the following packages:

• pandas==0.20.3
• scipy==0.19.1
• natsort==5.1.1
• numpy==1.13.3
• setuptools==38.4.0
• statsmodels==0.8.0

Run the following commands to clone and install from GitHub.

$ git clone https://github.com/mframpton/seqfam
$ cd seqfam
$ pip install -r requirements.txt
$ python setup.py install

Modules

Seqfam has 5 modules:

1. gene_drop.py: Monte Carlo gene dropping;
2. pof.py: variant pattern of occurrence in families;
3. gene_burden.py: regression-based gene burden testing;
4. relatedness.py: identification of duplicates and verification of ascertained pedigree information via kinship coefficients;
5. sge.py: Sun Grid Engine (SGE) array job creation.

Example scripts

The repository contains additional scripts in src/examples which demonstrate the functionality of the modules on example data, including files in the data directory. They are 1_example_gene_drop.py, 2_example_pof.py, 3_example_gene_burden.py, 4_example_relatedness.py, and 5_example_sge.py.

If the package is used to generate data for a publication, then please cite this article:

Matthew Frampton, Elena R. Schiff, Nikolas Pontikos, Anthony W. Segal, Adam P. Levine (2018) Seqfam: a python package for analysis of next generation sequencing DNA data in families. F1000Research https://f1000research.com/articles/7-281/v1