I created a pileup file from a list containing names of several bam files:
samtools mpileup -B -f ref.fa -b bam_list.txt > ouput.mpileup
The bam_list.txt looks like that:
Since the pileup format does not contain the individul IDs, it is difficult to know which columns correspond to what individual.
Does samtools give information following exactly the given list? E.g. columns 4 to 6 would correspond to Ind1.bam, 7 to 9, Ind2.bam ...etc (see example of pileup format: https://en.wikipedia.org/wiki/Pileup_format)
It's hard to tell and I need to make sure of what the order is.