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BRL-BCM / Allele-Registry

This repository contains the source code for the ClinGen Allele Registry. The Allele Registry provides unique identifiers for alleles. It can be accessed at https://reg.genome.network/.
GNU Affero General Public License v3.0
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Max duplicate size of 5k #6

Open davmlaw opened 2 months ago

davmlaw commented 2 months ago

It seems that duplicates are calculating their length to be twice as long as they should be (presumably ref == alt)

The ClinGen Allele Registry paper says:

The maximal nucleotide (transcript or genomic) allele size is 10,000 bp,

But:

NC_000017.11:g.43078305_43083385dup (length 5080) fails

while

NC_000017.11:g.43078305_43083300dup (length 4995) works

Meanwhile if you replace the "dup" with a "del" it works:

https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NC_000017.11%3Ag.43078305_43083385del

Presumably you could also insert a delisn between 5-10k but the moment the insertion is the same as the reference the size is halved