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Old 04-03-2013, 08:10 AM   #1
Location: US

Join Date: Dec 2012
Posts: 16
Default Snp calling between samples

There is a reference genome for subspecies A available. We did a resequencing for subspecies B and subspecies C using Hiseq 2000 and we'd like to know the SNP diversity(difference in allele frequency) between subspecies B and subspecies C.

We know there are substantial differences among subspecies A, B and C. So, what is the best way to find the SNP diversity between B and C? Should we do snp calling for subspecies B or C separately based on subspecies A reference genome (I used samtools) and then merge the results ? It seems to me we need a more efficient way to do the job but I don't know much (cortex ?).

Thanks in advance.
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