calling SNPs for prokaryotes

[Kasycas]

Hi,

I have genomic prokaryotic data and I want to look at SNPs between my data and the existing published data for very similar species. However, where MAQ worked well previously with Illumina data, I now have 454 reads and the BWA/samtools workflow with the pileup command seems to give information on different alleles where heterozygosity exists.

Has anyone worked with 454 data from a prokaryote to call SNPs and how so?

Thanks for the help!

[nickloman]

I tend to use the gsMapper component of Newbler (supplied by Roche with the 454 instrument) for SNP calling.

[Kasycas]

Thanks Nickloman. I hadn't used this part of Newbler before. I'll check it out.

[Kasycas]

Back on this topic, is GATK ok to use for the detection of prokaryotic SNPs with Illumina data? A lot of the information I'm reading refers to human data so I'm just worried I'd use it incorrectly.

The -D parameter worries me too as you need to specify a .rod file of which there seems only to be human versions...