Changes

=== '''How do I get reference files for an region of interest? '''  ===

=== '''How do I get reference files for an region of interest? '''  ===

#. For HapMapII format, download haplotypes from http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz

1. For HapMapII format, download haplotypes from http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz

#. For MACH format, you can do the following:  

2. 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