From Genome Analysis Wiki
Jump to navigationJump to search
183 bytes added
, 16:33, 18 June 2014
Line 78: |
Line 78: |
| The above command takes about 15 mins to finish. | | The above command takes about 15 mins to finish. |
| We will skip this step, and use a set of reference ancestry coordinates that have been generated in the file $HGDP/HGDP_938.RefPC.coord. | | We will skip this step, and use a set of reference ancestry coordinates that have been generated in the file $HGDP/HGDP_938.RefPC.coord. |
| + | View the reference coordinates: |
| | | |
| less -S $HGDP/HGDP_938.RefPC.coord | | less -S $HGDP/HGDP_938.RefPC.coord |
Line 89: |
Line 90: |
| Each sequenced sample will be projected from a 20-dimensional PCA space onto a 4-dimensional reference ancestry space. | | Each sequenced sample will be projected from a 20-dimensional PCA space onto a 4-dimensional reference ancestry space. |
| The running time is ~7 minutes for processing 3 samples in each job. | | The running time is ~7 minutes for processing 3 samples in each job. |
| + | |
| + | Step 2: Combine results |
| + | |
| + | cp hapmap_trios.1-3.SeqPC.coord hapmap_trios.SeqPC.coord |
| + | more +2 hapmap_trios.4-6.SeqPC.coord >> hapmap_trios.SeqPC.coord |