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, 16:08, 24 May 2010
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| | === '''Can I used unphased reference?''' === | | === '''Can I used unphased reference?''' === |
| | | | |
| − | A: Yes. You simply need a combined pedigree (.ped) and marker information file (.dat). <br> | + | A: Yes. You could create pedigree (.ped) and data files (.dat) that include both reference panel and sample genotypes or request that MaCH merge apppropriate files on the fly. |
| | | | |
| − | For example, if you have:
| + | For example, if you have: |
| | | | |
| − | '''ref.hap'''<br> ACGGA<br> CCGAA
| + | '''reference.dat''' |
| | + | M SNP1 |
| | + | M SNP2 |
| | + | M SNP3 |
| | + | M SNP4 |
| | + | M SNP5 |
| | | | |
| − | '''ref.snps'''<br> SNP1<br> SNP2<br> SNP3<br> SNP4<br> SNP5
| + | '''reference.ped''' |
| | + | REF1 REF1 0 0 1 A/C C/C G/G G/A A/A |
| | | | |
| − | '''sample.ped'''<br> 1 1 0 0 1 A/A G/G <br>
| + | '''sample.dat''' |
| | + | M SNP1 |
| | + | M SNP4 |
| | | | |
| − | '''sample.dat'''<br> M SNP1<br> M SNP4
| + | '''sample.ped''' |
| | + | 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 ./.
| + | Your could create a combined data set as: |
| | | | |
| − | '''comb.dat'''<br> M SNP1<br> M SNP2<br> M SNP3<br> M SNP4<br> M SNP5<br>
| + | '''comb.dat''' |
| | + | M SNP1 |
| | + | M SNP2 |
| | + | M SNP3 |
| | + | M SNP4 |
| | + | M SNP5 |
| | | | |
| − | <br>
| + | '''comb.ped''' |
| | + | REF1 REF1 0 0 1 A/C C/C G/G G/A A/A |
| | + | 1 1 0 0 1 A/A ./. ./. G/G ./. |
| | + | |
| | + | Equivalently, you could write -d reference.dat,sample.dat -p reference.ped,sample.ped on the command line and MACH would merge both files ''on-the-fly''. |
| | | | |
| | === '''More questions?''' === | | === '''More questions?''' === |
