Entering edit mode
3.5 years ago
salamonj9
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0
I've got a load of variants in HGVSp format. They're from this EBI dataset mutations.tsv (link near bottom of the page). How can I reliably parse them?
I've tried every tool I could find but absolutely none seem to support the square bracket deletion-insertion syntax which is frequently used: e.g. "Q45664:p.[Thr240Cys;Thr862Cys]". It looks like it is in the HGVS recommendations though.
I've tried Ensembl VEP, I've tried this Python HGVS parser and also this other one, but they all reject the square brackets.