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Revision as of 02:12, 9 December 2014
, 02:12, 9 December 2014→Interested in looking just at European/East Asian/Central South Asian populations?
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.
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 ==
