Changes

  # ./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

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.

Step 1: Place sequenced samples into the reference ancestry space:

Step 1: Place sequenced samples into the reference ancestry space:

  ./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 &

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.