I have reads from a bacterial sequence and I want to identify variants in them. I have performed an alignment using `bwa mem` and the reads aligned well. Is there a good pipeline for identifying SNPs, small indels etc in microbes? I could use mpileup but I don't find many people recommending that.
Well, dunno about other people, but I like `samtools mpileup`. It has always worked well for me in the microbial context:

    samtools mpileup -uf [genome] [bam] | bcftools view -vcg - > vcfs > [filename].vcf