Open davmlaw opened 3 months ago
The maximal nucleotide (transcript or genomic) allele size is 10,000 bp
43084385 - 43078305 = 6080 43083385 - 43078305 = 5080 - fails 43083300 - 43078305 = 4995 - this works
I think this is a bug with ClinGen Allele registry, have raised an issue with them and will use a work around until they fix it
The end result is that we fail early for ClinGen requests for dups over 5k, saving an API call - This is not really user testable
Not really user testable. SV pipelines have continued to run, make less API calls
Re-opening for Shariant testing Increases stability of liftover by not trying to contact ClinGen if there’s 5000+ base pair dups. Will fail ClinGen liftover, but will no longer block other variants in the queue.
Found while investigating SACGF/variantgrid_com#82
The SV pipeline does its own HGVS as VEP doesn't support symbolic variants
However it seems to run really slow. It errors with:
I thought the limit was 10k as 43084385 - 43078305 = 6080 so that should be ok
But even if you just enter it in the search you get VariationTooLong