Want to use samtools for polyploid organisms?

Well the short answer is you can't.
Here's what Heng Li has to say
Samtools is designed for diploid genomes. I would recommend to treat a haploid genome as diploid and filtering heterozygotes afterwards. For higher ploidy (>2), samtools does not work well. For pooled resequencing, specialized SNP callers (such as syzygy and a few others) are better.

Other recommendations are

• Freebayes (http://bioinformatics.bc.edu/marthlab/FreeBayes).
• CRISP http://polymorphism.scripps.edu/~vbansal/software/CRISP/