Converting vcf to pileup

Question

[sckinta]

I have vcf output from bayesfree and want to convert vcf output to pileup format which will be taken as input for popoolation2. Any script or software?

Thank you

[Devon Ryan]

VCF files won't typically contain all of the information required to generate a pileup of the original data. You'll need to do what Nicola Casiraghi wrote and simply make the pileup from the alignment files (assuming you have them).

Answer 1

[Nicola Casiraghi]

Hi, you can perform pileup using samtools mpileup and specifying with option -l your positions of interest.

[Sean Davis]

In other words, you'll need the BAM files.

[Nicola Casiraghi]

Yes exactly, mandatory inputs.