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From Genome Analysis Wiki
→How do I get reference files for an region of interest?
*Then:
@ first = `grep -n nw rsFIRST orig.snps | cut -f1 -d ':'` @ last = `grep -n nw rsLAST orig.snps | cut -f1 -d ':'`
*Finally (assuming the third field contains the actual haplotypes, where alleles are separated by whitespace):
