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How to filter Illumina Nirvana variant annotation?

Hello, we started to use Illumina Nirvana variant annotator for educational purposes. This annotator generates output in json format only. Please advice witch software compatible with json could I use for variant filtration?

Later we were used snpEff for annotation and GEMINI for filtration, but GEMINI does not work with json input and does not support hg38.

Thank you

nirvana filtration
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Kauno tvirtovės • Kauno tvirtovės

command-line tool is not a good decision for genomic data filtering nowadays

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written by Kauno tvirtovės • Kauno tvirtovės

command-line tool is not a good decision for genomic data filtering nowadays

whaaaaaaaaaaaaat ?

xkcd.com/285/

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written by Pierre Lindenbaum Pierre Lindenbaum

Clinical bioinformatics nowadays have a lot of plenty tools like https://franklin.genoox.com/ so I do not plan to waste time of my students with archaic command line pipelines.

Nirvana is quite good annotation engine with recommendation to use SnowFlake for filtering, but I have no experience how to do it.

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written by Kauno tvirtovės • Kauno tvirtovės

1 answer

hard to tell without seeing a sample of this json file. Otherwise there is jq: https://jqlang.github.io/jq/

furthermore in the doc they defined how you can find a delimiter bewteen VCF records, you can read by line using any custom program like python and accept/reject each json record

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written by Pierre Lindenbaum Pierre Lindenbaum

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