Question: opensource grafical user interface for filtering millions of annotated variant
1
gravatar for Aurélien Béliard
7 months 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 • 526 views
ADD COMMENTlink modified 7 months ago by Raony Guimarães820 • written 7 months 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 7 months ago by Pierre Lindenbaum112k
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 7 months ago by genomax55k

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 7 months ago by Aurélien Béliard10
3
gravatar for andrew.j.skelton73
7 months ago by
London
andrew.j.skelton735.3k 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 7 months ago by andrew.j.skelton735.3k
3
gravatar for Raony Guimarães
7 months ago by
Dublin / Ireland
Raony Guimarães820 wrote:

Hi there,

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

It's free and open source!

ADD COMMENTlink modified 7 months ago • written 7 months ago by Raony Guimarães820
1
gravatar for Hussain Ather
7 months ago by
Hussain Ather880
National Institutes of Health, Bethesda, MD
Hussain Ather880 wrote:

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

ADD COMMENTlink written 7 months ago by Hussain Ather880
1
gravatar for Pierre Lindenbaum
7 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum112k 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 7 months ago by Pierre Lindenbaum112k
0
gravatar for Pierre Lindenbaum
7 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum112k wrote:

galaxy https://usegalaxy.org/

ADD COMMENTlink written 7 months ago by Pierre Lindenbaum112k
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