SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
intersect VCF files adrian Bioinformatics 8 02-20-2014 12:36 PM
Annotating VCF files kasthuri Bioinformatics 7 07-16-2012 08:50 PM
Generating vcf files with samtools Brittd Bioinformatics 1 06-05-2012 11:41 PM
Merging vcf files kjaja Bioinformatics 0 01-12-2012 11:06 AM
merging VCF files kjaja Bioinformatics 2 12-20-2011 06:50 AM

Reply
 
Thread Tools
Old 02-04-2011, 12:05 PM   #1
mspivakov
Junior Member
 
Location: Cambridge

Join Date: Feb 2011
Posts: 2
Default Python API for VCF files

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:
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

Last edited by mspivakov; 02-04-2011 at 12:08 PM.
mspivakov is offline   Reply With Quote
Old 02-07-2011, 06:26 AM   #2
mspivakov
Junior Member
 
Location: Cambridge

Join Date: Feb 2011
Posts: 2
Default

Have now fixed a minor bug in VCFfilter.
Please re-download the module if you've already tried it.
mspivakov is offline   Reply With Quote
Old 02-02-2012, 02:33 AM   #3
casbon
Junior Member
 
Location: Cambridge, UK

Join Date: Sep 2011
Posts: 7
Default

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 is offline   Reply With Quote
Old 06-14-2012, 01:02 AM   #4
casbon
Junior Member
 
Location: Cambridge, UK

Join Date: Sep 2011
Posts: 7
Default

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 is offline   Reply With Quote
Old 06-27-2012, 12:54 AM   #5
casbon
Junior Member
 
Location: Cambridge, UK

Join Date: Sep 2011
Posts: 7
Default

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.
casbon is offline   Reply With Quote
Old 12-09-2013, 12:20 PM   #6
gourneau
Junior Member
 
Location: Tennessee

Join Date: Jan 2011
Posts: 2
Default

Thanks for the lib casbon
gourneau is offline   Reply With Quote
Old 04-07-2014, 09:35 AM   #7
FrankiB
Member
 
Location: Sherbrooke

Join Date: Dec 2013
Posts: 23
Default

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

Last edited by FrankiB; 04-07-2014 at 11:32 AM.
FrankiB is offline   Reply With Quote
Old 04-08-2014, 03:51 AM   #8
TiborNagy
Senior Member
 
Location: Budapest

Join Date: Mar 2010
Posts: 329
Default

If you have setuptools installed, you can use:
python setup.py install
TiborNagy is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:32 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO