ACMG assignment tools
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10 months ago
Eugene A ▴ 100

Hi, I've been asked to semi automate (as far as full automation of the process seems to be impossible) the ACMG annotations of WGS data for our clinicians.

What are the options here? I've checked several:

varsome (paid full access, closed code)

InterVar (seems nice, but works only with annovar, and I need to annotate ACMG terms on VEP output).

TAPES ( (recent paper, supposedly support VEP), but github page is dead and no response to the issues, crashes on exapmle files, so not an option.

Charger (investigating it right now - but the documentation is sparse :( ).

Am I missing something else here? Did anyone, by chance, had a luck to fit the VEP output to InterVar?

Best, Eugene

wes acmg WES WGS • 737 views
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Hey man... I'm stuck on the same subject as you! Did you find something usefull?

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Hi, eventually I decided for IntarVar (because of open source code + long git history) I re-write the code to make it cleaner for my pourpuses and used in combination with OpenCravat suit.

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That sounds interesting.. But how are you managing with the background databases???? I could not find documentation to upgrade it... Any thoughts???

Thanks, Vt

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Which one? InterVar internal db (lists of lof genes etc?) are still the same I have in mind to update these in the future. For cravat you need several available annotators and several custome, which I assembled from open sources (like dbnsfp)

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7 months ago

Hey, if you are still searching for ideas on how to implement the semi-automation, that you have described, you may also check autoPVS1 tool.

Edit: got to know some more ACMG tools! (also on 25.02.2021)

General Mendelian disease:

Cancer disease:

Hope it helps :)

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Thanks - I'll have a look!

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4 months ago

Hi, you can try varsome.com, there is an implementation of ACMG rules and you can query variants for free.

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It has too many restriction in the free version and in general has lack of flexability.

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