Variant calling for microbial genomes

Question

[Linda]

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.

Answer 1

[Dan D]

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

[Linda]

Do you just use the default parameters, or do you modify them in any way?

[Dan D]

It depends on what question I'm trying to answer, but the default parameters are a good starting point. From there you can survey your VCF, look for patterns that you want to investigate further or filter out, and then rerun the command accordingly.