genmod - Annotate genetic patterns of inheritance

Intro

genmod annotates patterns of inheritance in VCF files and handles arbitrary pedigrees. The idea is to set a standard for when we say that a certain pattern is followed and then annotate all variants as accurate as possible. This is a effective way to reduce the number of potential deleterious variants in family projects.

genmod is a leightweight, multiprocessing command line tool that can annotate millions of variants in minutes.

The genetic models that will be annotated are the following:

• Autsomal Recessive, denoted ‘AR’
• Autsomal Recessive denovo, denoted ‘AR_dn’
• Autsomal Dominant, ‘AD’
• Autsomal Dominant denovo, ‘AD_dn’
• Autosomal Compound Heterozygote, ‘AR_comp’
• Autosomal Compound Heterozygote, ‘AR_comp_dn’
• X-linked dominant, ‘XD’
• X-linked dominant de novo, ‘XD_dn’
• X-linked Recessive, ‘XR’
• X-linked Recessive de novo, ‘XR_dn’

Documentation

Documentation can be found at github. Example files and tests are included in the distribution

Installation

$ pip install genmod

or

$git clone git@github.com:moonso/genmod.git
$cd genmod
$python setup.py install

Then run

$ genmod

or try

$ genmod annotate examples/recessive_trio.ped examples/test_vcf.vcf

License

MIT

Credits

Tree by Grant Taylor from The Noun Project.