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Revision as of 11:52, 20 June 2014
, 11:52, 20 June 2014no edit summary
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_37224.laser.1.SeqPC.coord
Take a look:
evince Results_on_HGDP.pdf &
==Interested in looking just at European populations?==
=== Step 1: bam --> pileup ===
You can skip this, you already did it.
=== Step 2: pileup --> seq ===
python $LASER/pileup2seq/pileup2seq.py \
-m $HGDP/HGDP.633K.euro.site \
-o $OUT/ancestry/$SAMPLE.Euro.laser \
$OUT/ancestry/Sample_37224.recal.pileup
This step takes just a few seconds.
=== Estimate ancestry ===
This step will take a few seconds.
$LASER/laser -g $HGDP/HGDP.633K.euro.geno -c $HGDP/HGDP.633K.euro.RefPC.coord -s $OUT/ancestry/$SAMPLE.Euro.laser.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.Euro.laser.1 &
View the results:
less -S $OUT/ancestry/${SAMPLE}.Euro.laser.1.SeqPC.coord
== Visualizing Ancestry ==
Copy the R code to plot your ancestry
cp -r $LASER/plot/ $OUT/ancestry/.
Change to that new directory:
cd $OUT/ancestry/plot
Move your other plot so you don't over-write it
mv Results_on_HGDP.pdf Results_on_HGDP_All.pdf
Generate the plot:
Rscript plotHGDP.r $HGDP/HGDP.633K.euro.RefPC.coord $OUT/ancestry/${SAMPLE}.Euro.laser.1.SeqPC.coord
Take a look:
Take a look:
evince Results_on_HGDP.pdf &
evince Results_on_HGDP.pdf &
