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#. For HapMapII format, download haplotypes from http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz
#. For HapMapII format, download haplotypes from http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz
#. For MACH format, you can do the following:
#. For MACH format, you can do the following:
##. First, find the first and last SNP in the region you are interested in. Say "rsFIRST" and "rsLAST", defined according to position.
##. First, find the first and last SNP in the region you are interested in. Say "rsFIRST" and "rsLAST", defined according to position.
##. Then:
##. Then:
@ first = `grep -n rsFIRST orig.snps | cut -f1 -d ':'`
@ first = `grep -n rsFIRST orig.snps | cut -f1 -d ':'`
@ last = `grep -n rsLAST orig.snps | cut -f1 -d ':'`
@ last = `grep -n rsLAST orig.snps | cut -f1 -d ':'`
##. Finally (assuming the third field contains the actual haplotypes, where alleles are separated by whitespace):
##. Finally (assuming the third field contains the actual haplotypes, where alleles are separated by whitespace):
awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap
awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap
