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Revision as of 14:32, 13 November 2014
, 14:32, 13 November 2014no edit summary
'''Note:''' the latest version of this practical is available at: [[SeqShop: Ancestry On Your Own Genome]]
* The ones here is the original one from the June workshop (updated to be run from elsewhere)
{{SeqShopLogin}}
{{SeqShopLogin}}
Generate the plot:
Generate the plot:
Rscript plotHGDP.r $HGDP/HGDP_938.RefPC.coord $OUT/ancestry/Sample_37224.laser.1.SeqPC.coord
Rscript plotHGDP.r $HGDP/HGDP_938.RefPC.coord $OUT/ancestry/${SAMPLE}.laser.2.SeqPC.coord
Take a look:
Take a look:
evince Results_on_HGDP.pdf &
evince Results_on_HGDP.pdf &
==Interested in looking just at European populations?==
==Interested in looking just at European populations?==
-m $HGDP/HGDP.633K.euro.site \
-m $HGDP/HGDP.633K.euro.site \
-o $OUT/ancestry/$SAMPLE.Euro.laser \
-o $OUT/ancestry/$SAMPLE.Euro.laser \
$OUT/ancestry/Sample_37224.recal.pileup
$OUT/ancestry/${SAMPLE}.recal.pileup
This step takes just a few seconds.
This step takes just a few seconds.
