Question: opensource grafical user interface for filtering millions of annotated variant
1
gravatar for Aurélien Béliard
3.1 years ago by
Paris
Aurélien Béliard10 wrote:

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

sequencing snp • 1.5k views
ADD COMMENTlink modified 3.1 years ago by Raony Guimarães1.1k • written 3.1 years ago by Aurélien Béliard10

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.

ADD REPLYlink written 3.1 years ago by Pierre Lindenbaum134k
2

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.

ADD REPLYlink written 3.1 years ago by GenoMax96k

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.

ADD REPLYlink written 3.1 years ago by Aurélien Béliard10
3
gravatar for andrew.j.skelton73
3.1 years ago by
London
andrew.j.skelton736.1k wrote:

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

ADD COMMENTlink written 3.1 years ago by andrew.j.skelton736.1k
3
gravatar for Raony Guimarães
3.1 years ago by
Dublin / Ireland
Raony Guimarães1.1k wrote:

Hi there,

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

It's free and open source!

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Raony Guimarães1.1k
1
gravatar for Hussain Ather
3.1 years ago by
Hussain Ather950
National Institutes of Health, Bethesda, MD
Hussain Ather950 wrote:

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

ADD COMMENTlink written 3.1 years ago by Hussain Ather950
1
gravatar for Pierre Lindenbaum
3.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum134k wrote:

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...)

ADD COMMENTlink written 3.1 years ago by Pierre Lindenbaum134k
0
gravatar for Pierre Lindenbaum
3.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum134k wrote:

galaxy https://usegalaxy.org/

ADD COMMENTlink written 3.1 years ago by Pierre Lindenbaum134k
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