opensource grafical user interface for filtering millions of annotated variant

Question

[Aurélien Béliard]

Hi, I'am looking for an open source grafical user interface for filtering annotated variant. My principal constrain is that i have lots of variants. I need this software to be open source to add specific feature that we want. If you have some name or idea it will be very appreciated

[Pierre Lindenbaum]

My principal constraint is that i have lots of variants.

IMHO, your real problem is the GUI itself. A command-line is always better for this task.

[GenoMax]

Agreed. But a GUI may be preferable if Aurélien Béliard needs to give "non-command-line users" the ability to do some of the exploration themselves.

[Aurélien Béliard]

Pierre Lindenbaum the aim of this project is to allow our biologist user to filter and maybe annotate there variant themselve. We already have a software but he is very slow. i have found Varapp https://varapp-demo.vital-it.ch/docs/index.html varaft http://varaft.eu/ and some other but they seem to be limited in terme of variant number.

Answer 1

[andrew.j.skelton73]

I asked a similar question and compiled a list in another post - I updated it not long ago, so it's pretty current.

Answer 2

[Raony Guimarães]

Hi there,

Just want to say I made mendelmd.org for that.

It's free and open source!

Answer 3

[Hussain Ather]

VCF Miner https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793895/

Answer 4

[Pierre Lindenbaum]

another solution: using linux and zenity ( https://en.wikipedia.org/wiki/Zenity ) it's possible to create a simple interface for a linux cmd-line. Here is a GUI for my VCF filter vcffilterjdk: http://lindenb.github.io/jvarkit/VcfFilterJdk.html

(you just have to fix the path to vcffilterjdk.jar...)

Answer 5

[Pierre Lindenbaum]

galaxy https://usegalaxy.org/