Running BS-SNPer on multiple samples

[evoJDG]

Is there a way to call SNP variants across multiple files simultaneously with BS-SNPer?

It works fine with bam files containing data from a single sample but it does not accept multiple files as input. When I use a single bam file containing data from multiple samples (including read group information), BS-SNPer produces a single VCF file and does not appear to process the samples separately.

Thanks in advance.

James