Any update planned soon for AutoGVP?

[ChihyiLiao]

Hi AutoGVP team,

Thanks for maintaining AutoGVP.

I noticed there have been several recent ClinVar/InterVar-related issues and pull requests, so I just wanted to ask, is there any update or new release planned soon?

I also noticed two possible issues in the current workflow.

First, there may be an InterVar parsing issue in 02-annotate_variants_custom_input.R:

final_call_intervar = ifelse(
  intervar_adjusted == "No",
  sub(".*InterVar: ", "", sub("\\ P.*", "", `InterVar: InterVar and Evidence`)),
  ...
)

For a string like:

InterVar: Pathogenic PVS1=1 ...

sub("\\ P.*", "", ...) may remove Pathogenic as well, leaving only:

InterVar:

instead of:

Pathogenic

Second, I also ran into a possible formatting issue when the position is converted to scientific notation. For example, a position like:

62000000

may become:

6.20e+07

in an intermediate file, which can cause variant annotation or matching to fail.

Would these issues be addressed in the upcoming update?

Thanks!

[rjcorb]

Hi @ChihyiLiao -- thank you for submitting this ticket. We are planning on creating an AutoGVP v2 release in the next two weeks to incorporate the latest changes you've seen in tickets and PRs. One of these tickets actually addressed this scientific notation issue you've pointed out here. But I am going to work on resolving the other issue you've pointed out here. I will let you know once the updates are completed.

Thank you for using AutoGVP!

[jharenza]

Closed with #285

[ChihyiLiao]

Hi @ChihyiLiao -- thank you for submitting this ticket. We are planning on creating an AutoGVP v2 release in the next two weeks to incorporate the latest changes you've seen in tickets and PRs. One of these tickets actually addressed this scientific notation issue you've pointed out here. But I am going to work on resolving the other issue you've pointed out here. I will let you know once the updates are completed.

Thanks for the quick reply, and great to hear v2 is on the way!

Quick question: will AutoGVP v2 still rely on InterVar?
I ask because InterVar hasn't been updated in a while, which makes it inconvenient when I want to use newer databases (e.g. gnomAD v4.1 for the frequency criteria) or add new evidence (e.g. ESM1b scores for PP3/BP4). Just wondering whether v2 makes that any easier.

Thanks again for maintaining the tool!

[jharenza]

Quick question: will AutoGVP v2 still rely on InterVar?
I ask because InterVar hasn't been updated in a while, which makes it inconvenient when I want to use newer databases (e.g. gnomAD v4.1 for the frequency criteria) or add new evidence (e.g. ESM1b scores for PP3/BP4). Just wondering whether v2 makes that any easier.

Thanks again for maintaining the tool!

Hi @ChihyiLiao!

We recently made an update to update the intervar calls accounting for clinvar version (#289).

We don't have any immediate plans to rework it to exclude intervar. However, you can use gnomad4 as your filtering criteria for autogvp in general. Hope this helps!