From Genome Analysis Wiki
Jump to navigationJump to search
14 bytes added
, 15:43, 20 May 2010
Line 119: |
Line 119: |
| Estimated per allele error rate is 0.0293 | | Estimated per allele error rate is 0.0293 |
| | | |
− | A better approach is to mask a small proportion of SNPs (vs. genotypes in the above simple approach). One can generate a mask.dat from the original .dat file by simply changing the flag of a subset of markers from M to S2 without duplicating the .ped file. Post-imputation, one can use [http://www.sph.umich.edu/csg/ylwtx/CalcMatch.1.0.5.tgz CalcMatch ]and [http://www.sph.umich.edu/csg/ylwtx/doseR2.tgz doseR2.pl ]to estimate genotypic/allelic error rate and correlation respectively. Both programs can be downloaded from [http://www.sph.umich.edu/csg/ylwtx/software.html http://www.sph.umich.edu/csg/ylwtx/software.html]<br> | + | A better approach is to mask a small proportion of SNPs (vs. genotypes in the above simple approach). One can generate a mask.dat from the original .dat file by simply changing the flag of a subset of markers from M to S2 without duplicating the .ped file. Post-imputation, one can use [http://www.sph.umich.edu/csg/ylwtx/CalcMatch.1.0.5.tgz CalcMatch ]and [http://www.sph.umich.edu/csg/ylwtx/doseR2.tgz doseR2.pl ]to estimate genotypic/allelic error rate and correlation respectively. Both programs can be downloaded from [http://www.sph.umich.edu/csg/ylwtx/software.html http://www.sph.umich.edu/csg/ylwtx/software.html]<br> |
| | | |
| '''Warning''': Imputation involving masked datasets should be performed separately for imputation quality estimation. For production, one should use all available information.<br> | | '''Warning''': Imputation involving masked datasets should be performed separately for imputation quality estimation. For production, one should use all available information.<br> |
| + | |
| + | |
| | | |
| '''Q: How do I get reference files for an region of interest? '''<br> A: (1) For HapMapII format, download http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz <br> | | '''Q: How do I get reference files for an region of interest? '''<br> A: (1) For HapMapII format, download http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz <br> |