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genmod 0.9.5

Annotate genetic inheritance models in variant files

Latest Version: 2.0.12

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

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