Hello,
I am aligning whole genome read data against a reference in contigs with bfast as well as bwa. In both cases, I am finding a surplus of seeming snps at junction points (i.e. where N's span a break). Although concatenating and ridding of N's might help, it doesn't seem like an ideal solution. Is there a good way to eliminate said snps, i.e. identify junction points and eliminate snp's within 5 or so bp? Other thoughts?
I am aligning whole genome read data against a reference in contigs with bfast as well as bwa. In both cases, I am finding a surplus of seeming snps at junction points (i.e. where N's span a break). Although concatenating and ridding of N's might help, it doesn't seem like an ideal solution. Is there a good way to eliminate said snps, i.e. identify junction points and eliminate snp's within 5 or so bp? Other thoughts?