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, 02:12, 9 December 2014
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| evince Results_on_HGDP.pdf & | | evince Results_on_HGDP.pdf & |
| | | |
− | ==Interested in looking just at European/East Asian/Central South Asian populations?== | + | ==Interested in looking just at European or East Asian or Central South Asian populations?== |
| === Population information === | | === Population information === |
| 8 European populations in the HGDP dataset, including 156 individuals in total. | | 8 European populations in the HGDP dataset, including 156 individuals in total. |
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| This step will take a few seconds. | | This step will take a few seconds. |
| | | |
| + | For European ancestry: |
| $LASER/laser -g $HGDP/HGDP.633K.euro.geno -c $HGDP/HGDP.633K.euro.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP-Euro & | | $LASER/laser -g $HGDP/HGDP.633K.euro.geno -c $HGDP/HGDP.633K.euro.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP-Euro & |
| + | |
| + | For East Asian ancestry: |
| + | $LASER/laser -g $HGDP/HGDP.633K.easia.2.geno -c $HGDP/HGDP.633K.easia.2.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP-EAsia & |
| + | |
| + | For Central/South Asian ancestry: |
| + | $LASER/laser -g $HGDP/HGDP.633K.csasia.2.geno -c $HGDP/HGDP.633K.csasia.2.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP-CSAsia & |
| + | |
| | | |
| View the results: | | View the results: |
| less -S $OUT/ancestry/${SAMPLE}.HGDP-Euro.SeqPC.coord | | less -S $OUT/ancestry/${SAMPLE}.HGDP-Euro.SeqPC.coord |
| + | or |
| + | less -S $OUT/ancestry/${SAMPLE}.HGDP-EAsia.SeqPC.coord |
| + | or |
| + | less -S $OUT/ancestry/${SAMPLE}.HGDP-CSAsia.SeqPC.coord |
| | | |
| == Visualizing Ancestry == | | == Visualizing Ancestry == |