Availability of a robust, annotation-aware vcf-to-json converter
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6.2 years ago

Is anyone actively using a vcf-to-json converter that you would recommend?  I am aware of Variant Effect Predictor's ability to output json, but I am interested in something a little more generic and, ideally, one that handles snpEff annotations.  I wanted to check before putting something together myself.

json vcf variants ngs • 3.2k views
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6.2 years ago
Vincent Laufer ★ 1.4k

I cannot find one that is specifically compatible with SNPeff output. I dug around a bit, and only found the below, which is not as good as the VEP one, it seems.

https://github.com/pjotrp/bioruby-vcf/tree/master/lib 

Does VEP fail to work with SNPeff?  What language would you write this in? The folks at PyVCF might be interested...

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Great point about the PyVCF folks.

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please let me know what you plan to do. I am willing to help if decide to go python rather than R

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Python is the better tool for this job (of the two possibilities you mention).  I opened an issue with PyVCF.

https://github.com/jamescasbon/PyVCF/issues/204

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