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, 08:01, 18 May 2010
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| == FAQ == | | == FAQ == |
| + | |
| + | '''Q: Why and how to perform a 2-step imputation?'''<br> |
| + | |
| + | A: When one has a large number of individuals (>1000), we recommend a 2-step imputation to speed up. <br> |
| + | |
| + | A 2-step imputation contains the following 2 steps:<br> |
| + | |
| + | (step 1) a representative subset of >= 200 unrelated individuals are used to calibrate model parameters; and<br> (step 2) actual genotype imputation is performed for every person using parameters inferred in step 1. <br> |
| + | |
| + | Example command lines for a 2-step imputation:<br> |
| + | mach1 -d sample.dat -p subset.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip -r 100 -o par_infer > mach.infer.log |
| + | <br> |
| + | mach1 -d sample.dat -p sample.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip --errorMap par_infer.erate --crossoverMap par_infer.rec --mle --mldetails > mach.imp.log |
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| '''Q: Where can I find combined HapMap reference files? '''<br> A: http://www.sph.umich.edu/csg/yli/mach/download/HapMap-r21.html <br><br> | | '''Q: Where can I find combined HapMap reference files? '''<br> A: http://www.sph.umich.edu/csg/yli/mach/download/HapMap-r21.html <br><br> |
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| <br> | | <br> |
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− | '''Q: Can I used unphased reference?'''<br> | + | '''Q: Can I used unphased reference?'''<br> |
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− | A: Yes. You simply need a combined pedigree (.ped) and marker information file (.dat). <br> | + | A: Yes. You simply need a combined pedigree (.ped) and marker information file (.dat). <br> |
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− | For example, if you have: | + | For example, if you have: |
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− | '''ref.hap'''<br> ACGGA<br> CCGAA | + | '''ref.hap'''<br> ACGGA<br> CCGAA |
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− | '''ref.snps'''<br> SNP1<br> SNP2<br> SNP3<br> SNP4<br> SNP5 | + | '''ref.snps'''<br> SNP1<br> SNP2<br> SNP3<br> SNP4<br> SNP5 |
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− | '''sample.ped'''<br> 1 1 0 0 1 A/A G/G <br> | + | '''sample.ped'''<br> 1 1 0 0 1 A/A G/G <br> |
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− | '''sample.dat'''<br> M SNP1<br> M SNP4 | + | '''sample.dat'''<br> M SNP1<br> M SNP4 |
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− | The combined files should look like:<br> '''comb.ped'''<br> r1 r1 0 0 1 A/C C/C G/G G/A A/A<br> 1 1 0 0 1 A/A ./. ./. G/G ./. | + | The combined files should look like:<br> '''comb.ped'''<br> r1 r1 0 0 1 A/C C/C G/G G/A A/A<br> 1 1 0 0 1 A/A ./. ./. G/G ./. |
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− | '''comb.dat'''<br> M SNP1<br> M SNP2<br> M SNP3<br> M SNP4<br> M SNP5<br> | + | '''comb.dat'''<br> M SNP1<br> M SNP2<br> M SNP3<br> M SNP4<br> M SNP5<br> |
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| == Examples == | | == Examples == |