downsample vcf error

Question

[evafinegan]

Hello,

I am trying to downsample vcf file using:

java -jar /downsamplevcf.jar input.vcf -n 100 > subsample.vcf

But I get the error:

[INFO][Launcher]downsamplevcf Exited with failure (-1)

I will appreciate any help on this. Thank you!

[Pierre Lindenbaum]

 /downsamplevcf.jar

you put this file the root folder (?)

[Pierre Lindenbaum]

is it http://lindenb.github.io/jvarkit/DownSampleVcf.html ? I wrote that software for fun. I'm pretty sure that is not the only error message....

Answer 1

[Pierre Lindenbaum]

bcftools view --header-only  input.vcf > subsample.vcf
bcftools view --no-header input.vcf | awk '{printf("%f\t%s\n",rand(),$0);}' | sort -t $'\t' -k1,1g | cut -f2-  | head -n 1000 >>  subsample.vcf

[evafinegan]

Thank you! I am trying to subsample a vcf file by taking out the first 100 lines including header. I tried your suggestion using bcftools but it is not returning any output.