Skip to main content
Help us improve Python packaging – donate today!

probability of mendelian error in trios

Project Description

mendelian-error
===============

This package attempts to assign probability to a mendelian error event in a trio.
For example, given a mother with genotype 'C/C' and a father with genotype 'C/C'
a child with genotype 'C/T' will be a "mendelian error", in this case, a candidate
*de novo* mutation.

We can filter candidates based on their genotype likelihoods. For example if the
child had a genotype likelihood of -2,-1,-20 then we are likely to consider this
a genotyping error because the homozygous reference ("C/C" with GL -2) is fairly
close the the GL for het (with GL -1). If the genotype likelihood field was
-20,0,-20, then the call is confidently het. We can use the genotype likelihoods
to assign a probability:

```Python

>>> from mendelianerror import mendelian_error
# everyone is homref. this should have a low probability of an error:
>>> father = mother = child = [-0.1, -8.0, -8.0]
>>> mendelian_error(mother, father, child)
7.55...e-08


# parents are hom, child is het. this is a likely mendelian error:
>>> father = mother = [-0.6, -2.5, -2.5]
>>> child = [-2.5, -0.6, -2.5]
>>> mendelian_error(mother, father, child)
0.987...

```

So the input is the 3 GL numbers for each of the father, mother, child.

Installation
============

pip install mendelianerror

CLI
===

After installation, one can use this on a multi-sample VCF file like:
```Shell
mendelianerror $input.vcf father_id mother_id child_id > $new.vcf
```

to get only the putative mendelian errors, set a high cutoff:

```Shell
mendelianerror --cutoff 0.999 $input.vcf father_id mother_id child_id > $new.vcf
```


Limitations
===========

+ Only make sense for autosomal variants.
+ Only works on trios (doesn't consider extended pedigrees or siblings).

Release history Release notifications

This version
History Node

0.0.3

History Node

0.0.2

History Node

0.0.1

History Node

0.0.0

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
mendelianerror-0.0.3.tar.gz (4.5 kB) Copy SHA256 hash SHA256 Source None May 26, 2015

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page