As of samtools 0.1.8 'mpileup' appears to have superseded 'pileup' for variant detection. The samtools website now has pileup as deprecated.
So i am wondering whether i should repeat my recent SNP/INDEL calling with mpileup? But does anyone know what the improvements are using mpileup?
For those who don't already know 'pileup' and 'mpileup' can be used to create a consensus sequence using NGS mapped reads relative to a reference genome, but can also highlight variants relative to the reference.