pileup2vcf converter?

[a11msp]

Hi everyone,

So not reinvent the wheel, I'm wondering if there are any existing tools that can convert samtools pileup -c format to VCF?

I notice it's long been listed as an open task here (http://samtools.sourceforge.net/opentask.shtml), but surely many people had faced this problem - and have probably created a solution...

Many thanks!

[jts]

The latest samtools can output vcf through the mpileup program. Take a look at the samtools manual under the heading "Call SNPs and short indels for one diploid individual". I believe this the recommended way to call variants using samtools now.

http://samtools.sourceforge.net/samtools.shtml

[a11msp]

This is even better than what I was hoping to find, thanks a lot!