genmod - Annotate genetic patterns of inheritance
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 can be found at github.
Example files and tests are included in the distribution
$ pip install genmod
$ git clone firstname.lastname@example.org:moonso/genmod.git $ cd genmod $ python setup.py install
$ genmod annotate examples/recessive_trio.ped examples/test_vcf.vcf
See the code for genmod here: https://github.com/moonso/genmod