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, 16:23, 18 June 2014
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| # ./LASER-2.01/laser -g ./HGDP/HGDP_938.geno -pca 1 -k 30 -o HGDP_938 | | # ./LASER-2.01/laser -g ./HGDP/HGDP_938.geno -pca 1 -k 30 -o HGDP_938 |
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− | The above command takes about 15 mins to finish and we will skip it in this tutorial. A set of reference ancestry coordinates has been generated in the file $HGDP/HGDP_938.RefPC.coord. | + | 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. |
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| Step 1: Place sequenced samples into the reference ancestry space: | | Step 1: Place sequenced samples into the reference ancestry space: |
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| ./LASER-2.01/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s hapmap_trios.seq -K 20 -k 4 -x 4 -y 6 -o hapmap_trios.4-6 & | | ./LASER-2.01/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s hapmap_trios.seq -K 20 -k 4 -x 4 -y 6 -o hapmap_trios.4-6 & |
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− | The first job will process samples 1 to 3 and the second job will processed samples 4 to 6. 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 first job will process samples 1 to 3 and the second job will processed samples 4 to 6. |
| + | 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. |