Hello,

I've done a multi-sample SNP calling with samtools mpileup, and my results are in a vcf file.

I would like to keep only SNPs detected on all of my samples (without any sample with GT flag = 0/0 ,(homozygote for the reference allele)).

Does anyone know a tool that could do it?

Thanks!
<p>I usually choose vcftools or bcftools to deal with vcf files, but in your case a simple <em>grep</em> would do:</p>

<pre>
grep -v &quot;0[/|]0&quot; &lt;in.vcf &gt;out.vcf</pre>
