Downsample vcf file

[MurielGB]

Hello !

Is there a tool available to randomly select let's say 1,000 snps in a vcf file ?
Thank you !

Muriel

[cariboudoug]

Hey,

This might be helpful: https://www.biostars.org/p/16038/

If each line of your vcf is a different SNP you can do:
shuf -n 1000 X.vcf

Otherwise you could parse out only variant positions into a new file first.

Gavin

[lindenb]

I wrote one: https://github.com/lindenb/jvarkit/wiki/DownSampleVcf

[MurielGB]

Hi all !

Thanks a lot for your answers.
Lindenb, I would like to use your tool but don't manage to install it...

I tried to follow the installation but it doesn't work.

I did :

git clone "https://github.com/lindenb/jvarkit.git"
cd jvarkit

git submodule init
git submodule update
git submodule foreach git pull origin master

But then I am supposed to move into a directory (cd htsjdk) but it doesn't exist...

Can you help ? This tools looks awesome !!
Thank you !

Muriel