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Python API for VCF files

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  • 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, 01:08 PM.

  • #2
    Have now fixed a minor bug in VCFfilter.
    Please re-download the module if you've already tried it.

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    • #3
      I have a python VCF parser up on github, if that helps. Check the pyvcf documentation. There is an extensible VCF filter as well.

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      • #4
        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

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        • #5
          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.

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          • #6
            Thanks for the lib casbon

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            • #7
              Is it working with python 3.3 and if yes, where can I find instructions for installation?
              Last edited by FrankiB; 04-07-2014, 11:32 AM.

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              • #8
                If you have setuptools installed, you can use:
                python setup.py install

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