SACGF / SACGF/variantgrid

Biocommons - variant over alignment gap

Open
#1,353 2 comments 0 reactions 1 assignee Claimed by @davmlaw View on GitHub
Dominant language
Python
Stars
30
Forks
3
Avg merge
9h 28m
Merged PRs (30d)
42

Description

Raising an issue as this was lost in another issue that has been re-purposed to test Biocommons generally. These variants exist when a variant is over an alignment gap/insertion/etc. See the following examples:

NM_130444.3(COL18A1):c.4078_4086delGGCCCCCCA
NM_015120.4(ALMS1):c.72_77delGGAGGA
NM_015120.4(ALMS1):c.75_77dupGGA

I think the simplest way forward would be to detect and error, similarly to what is done in pyhgvs currently.

This issue has already been raised in biocommons, but we are waiting on a reply - https://github.com/biocommons/hgvs/issues/758

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.