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!
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!
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