From Genome Analysis Wiki
Jump to navigationJump to search
110 bytes removed
, 16:12, 24 May 2010
Line 136: |
Line 136: |
| === '''How do I get reference files for an region of interest? ''' === | | === '''How do I get reference files for an region of interest? ''' === |
| | | |
− | A: (1) For HapMapII format, download http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz <br>
| + | #. For HapMapII format, download haplotypes from http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz |
| | | |
− | (2) For MACH format, you can do the following:
| + | #. For MACH format, you can do the following: |
| | | |
− | (2-1) 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. |
| | | |
− | (2-2) 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 ':'` |
| | | |
− | (2-3) Finally (assuming the third field contains the actual haplotypes, where alleles are separated by nothing):
| + | ##. 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 |