How to filter Illumina Nirvana variant annotation?

Question

[Kauno tvirtovės]

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

[Kauno tvirtovės]

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

[Pierre Lindenbaum]

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

whaaaaaaaaaaaaat ?

[Kauno tvirtovės]

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.

[Pierre Lindenbaum]

archaic command line pipelines.

'speechless'

Answer 1

[Pierre Lindenbaum]

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