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

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
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updated by Ram Ram • written by Sean Davis Sean Davis

1 answer

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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updated by Ram Ram • written by LauferVA LauferVA

Great point about the PyVCF folks.

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written by Sean Davis Sean Davis

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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written by LauferVA LauferVA

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