Changes

SeqShop: Estimates of Genetic Ancestry Practical, December 2014 (view source)

18 bytes removed , 00:54, 8 December 2014

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LASER can perform principal components analysis (PCA) on genotype data of the reference panel to generate a reference ancestry space.

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# ./LASER~~-2.01~~/laser -g $HGDP/HGDP_938.geno -pca 1 -k 30 -o HGDP_938

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# $LASER/laser -g $HGDP/HGDP_938.geno -pca 1 -k 30 -o HGDP_938

The above command takes ~20 minutes to finish.

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Submit two jobs to 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 1 -y 3 -o hapmap_trios.1-3 &

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$LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s hapmap_trios.seq -K 20 -k 4 -x 1 -y 3 -o hapmap_trios.1-3 &

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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 &

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$LASER/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.

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