issue about microbial variant detection

[anyone1985]

I use gatk, freebayes and samtools to calling the variant from microbial sequence. According to the common sense, I think I should use the haploid model like gatk or freebayes. However, several literature say that it's good to use samtools to call variant, which was designed for polyploid. I'd like to know should I use the haploid model of gatk and freebayes or just use the default parameters of the three methods to call variant for microbial. I'm not familiar with the algorithm,

[SylvainL]

Hi, do you know how many copies of chromosome your bacterium has? Usually for microbial SNPs/InDels calling, I use freebayes set to haploid but sometimes, like for a Synechocystis project (around 10 copies of the same chromosome), results were nicer considering 10 copies of the genome...

[anyone1985]

I do not know the copies of chromosome. My subject is Mycobacterium tuberculosis. In the following papers, they used samtools. I will compare the results from gatk and freebayes (haploid model) and samtools (default parameters). I'd like to know whether there is anyone has done this before.

http://www.ncbi.nlm.nih.gov/pubmed/26116186

http://www.ncbi.nlm.nih.gov/pubmed/25732036