Python API for VCF files

[mspivakov]

Hi everyone,

I wanted to share with you a prototype Python module for parsing and filtering VCF files. It was tested on pooled files generated by GATK UnifiedGenotyper (ie, they contain both pool-level and sample-level fields), but it shouldn't require much tweaking (if at all) for use with VCFs generated by other tools.

The module and a short tutorial can be downloaded from here:

https://www.ebi.ac.uk/~spivakov/vcf_v0.1.zip

Please let me know if you find it useful or have any comments/suggestions.

Cheers,
Mikhail

[mspivakov]

Have now fixed a minor bug in VCFfilter.
Please re-download the module if you've already tried it.

[casbon]

I have a python VCF parser up on github, if that helps. Check the pyvcf documentation. There is an extensible VCF filter as well.

[casbon]

Just a quick update, I have released the last pyvcf in the 0.4 release http://pyvcf.readthedocs.org/en/late...Y.html#release

I'm now considering VCF 4.1 and SV support, if you have any experience with these types of data, help us flesh out the API:

https://github.com/jamescasbon/PyVCF/issues/17

[casbon]

I just released PyVCF 0.5.0. This release brings VCF 4.1 Support, including support for structural variation and breakends. It includes many improvements to the VCF writer, a new utility vcf_melt and a new set of filters. You can see the full list of changes.

Thanks very much to @dzerbino, @lennax, @libor-m, @ilyaminkin and @martijnvermaat for help on this release.

[gourneau]

Thanks for the lib casbon

[FrankiB]

Is it working with python 3.3 and if yes, where can I find instructions for installation?

[TiborNagy]

If you have setuptools installed, you can use:
python setup.py install