Software for clinical interpretation of variants

Question

[SunRise2019]

I do have a long list of variants and would like to know which software or database is considered standard for clinical interpretation, particularly whether there is a drug used when this variant is found, I know there is: ClinVar, COSMIC, and some paid stuff (Qiagen Insight Interpret) but I think there must be other free databases/software/websites with more information and which experts in the field consider "standard".

Would appreciate any input.

Answer 1

[steve]

As far as databases, I have also used PMKB ( https://pmkb.weill.cornell.edu/ ) in the past, and there is also OncoKB ( https://www.oncokb.org/ ). I was going to mention N-of-One but it seems like Qiagen has already acquired them so maybe its bundled into the platform you mentioned.

For software, well you will definitely want VEP ( https://useast.ensembl.org/info/docs/tools/vep/index.html ) to apply the annotations from some of those available databases to your variants. I have used ANNOVAR in the past and always end up wishing I had used VEP instead. For databases that you cannot pull in with VEP/ANNOVAR/etc., you can always just build your own tools.

[SunRise2019]

Thanks! Could you tell me why you wished you had used VEP instead. What was missing with ANNOVAR that you find with VEP? Thanks!

[steve]

ANNOVAR works fine and has great features. Most of my issues end up coming from the licensing required for ANNOVAR for commercial use (you start building some small pipeline then suddenly your company/institute wants to deploy it as part of a product), and also the input & output formats. I end up spending a lot of time fiddling with the variant tables to get them into ANNOVAR format then again getting the ANNOVAR output back into a good format for downstream use. Whereas VEP has always seemed a lot more flexible about both inputs and outputs. Also VEP has seemed to simply be more widespread, maybe due to the licensing, external collaborators and vendors I have worked with were all using VEP and so it made it extra annoying when trying to compare variant outputs that I had annotated with ANNOVAR.

[SunRise2019]

Thanks, this makes it clear! I have just tested VEP and found it great. I was just wondering whether there is a piece of free software out there that provides copy number data (CNV) from whole exome sequencing..