I have mapped and SNP called using a cDNA reference and using a draft complete reference of many contigs of the same species. I would like to compare the two SNP files and identify common found snps between the two files and unique. Usually I would use vcf tools for SNPs generated using the same reference but these references will not have the same positions or necessary exact sequences.
I was planning on generated a perl script that would take 200 bp either side of the called SNP position and called SNP so a 401bp sequence from one reference then blasting for that in the other reference (decypher installed at my work) then with the resulting output take the top hit and search again within this sequence for a smaller sequence say 21bp including the SNP, if this is found to confirm the location then print to file and identifer as common. I was wondering if someone had done something similar or knew of available software that would do this?
