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, 15:09, 30 April 2010
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| Q: How do I get reference files for an region of interest? <br> | | Q: How do I get reference files for an region of interest? <br> |
− | A: For HapMapII format, download http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz | + | A: For HapMapII format, download http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz <br> |
− | 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. |
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| 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 ':'` |
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| 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 nothing): |
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− | 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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| == Examples == | | == Examples == |