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Revision as of 14:57, 21 May 2015
, 14:57, 21 May 2015→Visualizing Ancestry
'''Setup LASER'''
'''Setup LASER'''
export SSREF=/net/seqshop-server/home/mktrost/seqshop/singleSample/ref
export SSREF=/net/seqshop-server/home/mktrost/seqshop/singleSample/ref
export LASER=$OUT/ancestry/LASER-2.01
export LASER=~/seqshop/output/ancestry/LASER-2.01
(SAMPLE & OUT were previously set in your screen session.)
(SAMPLE were previously set in your screen session.)
After setting this, also do
After setting this, also do
Ctrl-a d
Ctrl-a d
While that's running, let's go run the Association Analysis Practical: [[SeqShop: Genetic Association Analysis Practical, December 2014]]
While that's running, let's go look at Calling results: [[ SeqShop: Calling Your Own Genome, May 2015]]
=== Checking if Pileup finished ===
=== Checking if Pileup finished ===
python $LASER/pileup2seq/pileup2seq.py \
python $LASER/pileup2seq/pileup2seq.py \
-m $SSREF/HGDP_938.site \
-m $SSREF/HGDP/HGDP_938.site \
-o $OUT/ancestry/$SAMPLE.HGDP \
-o $OUT/ancestry/$SAMPLE.HGDP \
$OUT/ancestry/$SAMPLE.HGDP.pileup
$OUT/ancestry/$SAMPLE.HGDP.pileup
This step will take about 5-6 minutes.
This step will take about 5-6 minutes.
$LASER/laser -g $SSREF/HGDP_938.geno -c $SSREF/HGDP_938.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP &
$LASER/laser -g $SSREF/HGDP/HGDP_938.geno -c $SSREF/HGDP/HGDP_938.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP &
View the results:
View the results:
Generate the plot:
Generate the plot:
Rscript plotHGDP.r $HGDP/HGDP_938.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP.SeqPC.coord
Rscript plotHGDP.r $SSREF/HGDP/HGDP_938.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP.SeqPC.coord
Take a look:
Take a look:
For European ancestry:
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 $SSREF/HGDP/HGDP.633K.euro.geno -c $SSREF/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:
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 &
$LASER/laser -g $SSREF/HGDP/HGDP.633K.easia.2.geno -c $SSREF/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:
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 &
$LASER/laser -g $SSREF/HGDP/HGDP.633K.csasia.2.geno -c $SSREF/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 &
Generate the plot for European ancestry:
Generate the plot for European ancestry:
Rscript plotHGDP.r $HGDP/HGDP.633K.euro.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP-Euro.SeqPC.coord
Rscript plotHGDP.r $SSREF/HGDP/HGDP.633K.euro.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP-Euro.SeqPC.coord
or for East Asian ancestry
or for East Asian ancestry
Rscript plotHGDP.r $HGDP/HGDP.633K.easia.2.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP-EAsia.SeqPC.coord
Rscript plotHGDP.r $SSREF/HGDP/HGDP.633K.easia.2.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP-EAsia.SeqPC.coord
or for Central/South Asian ancestry
or for Central/South Asian ancestry
Rscript plotHGDP.r $HGDP/HGDP.633K.csasia.2.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP-CSAsia.SeqPC.coord
Rscript plotHGDP.r $SSREF/HGDP/HGDP.633K.csasia.2.RefPC.coord $OUT/ancestry/${SAMPLE}.HGDP-CSAsia.SeqPC.coord
Take a look:
Take a look:
