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, 11:52, 20 June 2014
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| 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 & |