[Samtools-help] How to set -N in pileup command for bacterial genomes?

[Rasmus L. M. N. <rn...@bi...>]

Hello,

Should the [-N] option in the samtools pileup command be set to  "1" instead of default "2" when analyzing bacterial genomes. I understand it as a bacterial genome is haploid and not diploid as the human genome, however I see that the -N option should only be 2 or greater.

I have been using samtools to do SNP detection in resequenced bacterial genomes (<200 SNPs expected per genome of 6 Mb).

Thanks. Rasmus