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Annotate genetic inheritance models in variant files

Project description

GENMOD
======

Tool for annotating patterns of inheritance Variant Call Format (VCF)
files.

Each variant in the VCF-file will be annotated with which genetic models
that are followed in the family. The genetic models that are checked 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'
- X-linked dominant, 'XD'
- X-linked dominant de novo, 'XD\_dn'
- X-linked Recessive, 'XR'
- X-linked Recessive de novo, 'XR\_dn'

**GENMOD** will add entrys to the INFO column for the given VCF file.
The new entrys are:

- GM: A colon separated list with genetic models followed
- ANN: Colon separated list with features overlapped in the annotation
file
- Comp: Colon separated list with compound pairs(if any). These are
described like CHR\_POS\_REF\_ALT.
- MS: Model Score, a phred-score based on the genotype qualities to
describe the uncertainty of the genetic model.

Installation:
-------------

genmod works with Python 2.7 and Python 3.

::

pip install genmod

or

::

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

USAGE:
~~~~~~

::

genmod ped_file variant_file annotation_file

Conditions for Genetic Models
-----------------------------

Short explanation of genotype calls in VCF format:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Since we only look at humans, that are diploid, the genotypes represent
what we see on both alleles in a single position. 0 represents the
reference sequence, 1 is the first of the alternative alleles, 2 second
alternative and so on. If no phasing has been done the genotype is an
unordered pair on the form x/x, so 0/1 means that the individual is
heterozygote in this given position with the reference base on one of
the alleles and the first of the alternatives on the other. 2/2 means
that we see the second of the alternatives on both alleles. Some
chromosomes are only present in one copy in humans, here it is allowed
to only use a single digit to show the genotype. A 0 would mean
reference and 1 first of alternatives.

If phasing has been done the pairs are not unordered anymore and the
delimiter is then changed to '\|', so one can be heterozygote in two
ways; 0\|1 or 1\|0.

Autosomal Recessive
~~~~~~~~~~~~~~~~~~~

For this model individuals can be carriers so healthy individuals can be
heterozygous. Both alleles need to have the variant for an individual to
be sick so a healthy individual can not be homozygous alternative and a
sick individual *has* to be homozygous alternative.

- Affected individuals have to be homozygous alternative (hom. alt.)
- Healthy individuals cannot be hom. alt.
- Variant is considered *de novo* if both parents are genotyped and do
not carry the variant

Autosomal Dominant
~~~~~~~~~~~~~~~~~~

- Affected individuals have to be heterozygous (het.)
- Healthy individuals cannot have the alternative variant
- Variant is considered *de novo* if both parents are genotyped and do
not carry the variant

Autosomal Compound Heterozygote
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This model includes pairs of variants that are present within the same
feature.

1. Non-phased data:

- Affected individuals have to be het. for both variants
- Healthy individuals can be het. for one of the variants but cannot
have both variants
- Variant is considered *de novo* if only one or no variant is found
in the parents

2. Phased data:

- All affected individuals have to be het. for both variants and the
variants has to be on two different alleles
- Healthy individuals can be heterozygous for one or both of the
variants if they are on the allele
- If only one or no variant is found in parents it is considered *de
novo*

X-Linked Dominant
~~~~~~~~~~~~~~~~~

These traits are inherited on the x-chromosome, of which men have one
allele and women have two.

- Variant has to be on chromosome X
- Affected individuals have to be het. or hom. alt.
- Healthy individuals cannot carry the variant
- If sex is male the variant is considered *de novo* if mother is
genotyped and does not carry the variant
- If sex is female variant is considered *de novo* if none of the
parents carry the variant

X Linked Recessive
~~~~~~~~~~~~~~~~~~

- Variant has to be on chromosome X
- Affected individuals have to be het. or hom. alt.
- Healthy individuals cannot be hom. alt.
- If sex is male the variant is considered *de novo* if mother is
genotyped and does not carry the variant
- If sex is female variant is considered *de novo* if not both parents
carry the variant

.. raw:: html

<!-- ## Detailed Structure ##

Here all attributes and methods of the classes will be showed:

### Genotype ###

Store the genotype information of a variant that is specific for an individual

**Attributes:**

* genotype STRING
* allele_1 STRING
* allele_2 STRING
* nocall BOOL
* heterozygote BOOL
* homo_alt BOOL
* homo_ref BOOL
* has_variant BOOL
* filter STRING
* ref_depth INT
* alt_depth INT
* phred_likelihoods TUPLE with INT
* depth_of_coverage INT
* genotype_quality FLOAT


### Variant ###

Holds the info of a variant and it's specific behaviour in a family.

**Attributes**

* chr STRING Have to be string since X, Y
* start INT
* stop INT
* ref STRING Reference nucleotide(s)
* alt STRING Alternative sequence
* identity STRING dbSNP-id
* var_info DICT A dictionary with all the info from the variant file
* qual STRING A value for the score of the base call
* filter STRING The filter status
* genotypes LIST A list with the genotypes found for this variants
* gene STRING Semicolon separated string with ensemble gene names
* ad BOOL If following Autosomal Dominant pattern
* ad_dn BOOL If following Autosomal Dominant De novo pattern
* ar BOOL If following Autosomal Recessive pattern
* ar_dn BOOL If following Autosomal Recessive De nove pattern
* ar_comp BOOL If following Autosomal Recessive compound pattern
* ar_comp_dn BOOL If following Autosomal Recessive Compound De Novo pattern

**Methods**

* get_variant(self):
Returns a dictionary with basic info to stdout
* print_model_info(self):
Print for each variant which patterns of inheritance they follow.
* print_vcf_variant(self):
Print the variant in vcf-format to stdout
* print_original_version(self, header_columns):
Prints the variant in its original format.
* check_noncomplete_call(self):
Check if GATK have missed to report some info.
* get_genotype(self):
Returns the list with genotypes for this variant.


### Individual ###

Holds the information about an individual and the individual specific genotypes.

**Attributes**

* ind STRING Can be any id unique within the family
* family STRING Can be any unique id within the cohort
* mother STRING The ind_id of the mother or [0,-9] if info is missing
* father STRING ---------||------ father --------------||---------------
* sex INT 1=male 2=female 0=unknown
* phenotype INT 1=unaffected, 2=affected, missing = [0,-9]
* genotypes DICT Container with genotype information on the form {<variant_id>: <Genotype>}
* phasing BOOL If the genotype information includes phasing for this individual

### Family ###

**Attributes**

* individuals DICT dictionary with family members on the form {<ind_id>:<Individual>}
* variants DICT dictionary with all the variants that exists in the family on the form {<var_id>:<Variant>} -->

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