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inheritance models for mendelian genetics

Project description

inheritance models for mendelian diseases

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This module is a general-purpose framework for evaluating if a family exihibits, for example, and autosomal dominant pattern.
The logic for this was tuned in [gemini]( but we make it available here as a more general purpose library to encourage:
1. community driven improvements
2. use outside of gemini
3. more comprehensive testing

Finding variants that match autosomal dominance in a trio, for example is very simple to find,
however, after considering multiple generations, arbitrary family sizes, depth cutoffs, and unknown
genotypes and phenotypes to support to real-world datasets it becomes tedious and error-prone.

Supported inheritance tests

+ autosomal dominant
+ autosomal recessive
+ de novo
+ X-linked dominant, recessive, and de novo
+ compound heterozygote
+ mendelian violation


For now, the use is via api only. Users can look at the tests to see how to use. Most functions have a signature like:

auto_dom(self, min_depth=0, gt_ll=False, strict=True, only_affected=True)

where the arguments enforce a minimum depth, a maximum genotype likelihood, strictness (mostly related to parent-offspring requirements)
and wether to allow unaffecteds to have the variant (or be homozygous alt).

1. add support for X-linked soon.
2. add a simple example of running on a VCF+PED
3. code coverage
4. code documentation


Tests can be run as:

nosetests --with-coverage -x --with-doctest --cover-package inheritance


the generic code is in `inheritance/` and a specific implementation that we use in gemini is in `inheritance/`.
To make this available for a new resource, for example to `bcftools` we would look at the implementation of Filter in `inheritance/`
and make the generated strings match those expected by `bcftools`.

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