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opensource grafical user interface for filtering millions of annotated variant

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
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updated by Raony Guimarães Raony Guimarães • written by Aurélien Béliard • Aurélien Béliard

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.

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written by Pierre Lindenbaum Pierre Lindenbaum

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.

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written by GenoMax GenoMax

5 answers

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

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written by andrew.j.skelton73 andrew.j.skelton73

Hi there,

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

It's free and open source!

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written by Raony Guimarães Raony Guimarães

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

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written by Hussain Ather Hussain Ather

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...)

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written by Pierre Lindenbaum Pierre Lindenbaum

galaxy https://usegalaxy.org/

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written by Pierre Lindenbaum Pierre Lindenbaum

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