ENSVAR-6654 & ENSVAR-6381

[olaaustine]

#Ensembl/ensembl-vep#1710
#Ensembl/ensembl-vep#1796

[jamie-m-a]

Hi Ola, I don't think we need to roll this back completely, it was added to address the situations described in: #1066

I don;t agree with all of Nuno's use case examples, but the stop retained examples of * to * in the same position should be captured and can be with something like:

($ref_pep eq substr($alt_pep, 0, 1) && $alt_pep =~ /\*/ && $ref_pep =~/\*/ && pos($alt_pep) == pos($ref_pep))

I tested it on the GRCh37 examples linked in this ticket and it correctly returns stop_gained as the top consequence. It also returned stop_retained for the first example Nuno gave (6 30590698 . GTGA CTAG on GRCh38).

Could you check it out a bit more on some more tests - thanks

[olaaustine]

Hi Ola, I don't think we need to roll this back completely, it was added to address the situations described in: #1066

I don;t agree with all of Nuno's use case examples, but the stop retained examples of * to * in the same position should be captured and can be with something like:

($ref_pep eq substr($alt_pep, 0, 1) && $alt_pep =~ /\*/ && $ref_pep =~/\*/ && pos($alt_pep) == pos($ref_pep))

I tested it on the GRCh37 examples linked in this ticket and it correctly returns stop_gained as the top consequence. It also returned stop_retained for the first example Nuno gave (6 30590698 . GTGA CTAG on GRCh38).

Could you check it out a bit more on some more tests - thanks

Hi Jamie,
With more tests, this change will not capture all examples of stop retained especially with the first issue, I am going to keep investigating to figure out the best possible way around this.
I do not want to hold up the branching so we can always rebase as already discussed during standup.
Thanks

[jamie-m-a]

Agreed Ola, we shouldn’t rush this change, thanks for taking a look.

…

On 6 Feb 2025, at 12:10, Ola Austine ***@***.***> wrote: Hi Ola, I don't think we need to roll this back completely, it was added to address the situations described in: #1066 <#1066> I don;t agree with all of Nuno's use case examples, but the stop retained examples of * to * in the same position should be captured and can be with something like: ($ref_pep eq substr($alt_pep, 0, 1) && $alt_pep =~ /\*/ && $ref_pep =~/\*/ && pos($alt_pep) == pos($ref_pep)) I tested it on the GRCh37 examples linked in this ticket and it correctly returns stop_gained as the top consequence. It also returned stop_retained for the first example Nuno gave (6 30590698 . GTGA CTAG on GRCh38). Could you check it out a bit more on some more tests - thanks Hi Jamie, With more tests, this change will not capture all examples of stop retained especially with the first issue , I am going to keep investigating to figure out the best possible way around this. I do not want to hold up the branching so we can always rebase as already discussed during standup. Thanks — Reply to this email directly, view it on GitHub <#1149 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMFCBGVOMQ62D7UXGBMLJBD2ONGLXAVCNFSM6AAAAABWHSXQ6OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMZZGY2TAOJYGU>. You are receiving this because your review was requested.

[jamie-m-a]

Can rebase now