Question

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

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8.7 years ago

Sean Davis 26k

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.

ngs vcf json variants • 4.1k views

ADD COMMENT • link updated 18 months ago by Ram 43k • written 8.7 years ago by Sean Davis 26k

Ram · Answer 1 · 2015-08-07

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8.7 years ago

LauferVA 4.2k

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...

ADD COMMENT • link updated 18 months ago by Ram 43k • written 8.7 years ago by LauferVA 4.2k

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Great point about the PyVCF folks.

ADD REPLY • link 8.7 years ago by Sean Davis 26k

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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

ADD REPLY • link 8.7 years ago by LauferVA 4.2k

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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

ADD REPLY • link updated 18 months ago by Ram 43k • written 8.7 years ago by Sean Davis 26k