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Revision as of 16:33, 18 June 2014
, 16:33, 18 June 2014→Estimating ancestry coordinates using LASER
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
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
