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, 16:13, 24 May 2010
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| === '''How do I get reference files for an region of interest? ''' === | | === '''How do I get reference files for an region of interest? ''' === |
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− | #. 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 |
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