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?
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).
Hi, you can perform pileup using samtools mpileup and specifying with option -l your positions of interest.
In other words, you'll need the BAM files....
Yes exactly, mandatory inputs.