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| + | '''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}} |
| | | |
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| OUT needs to point to where your alignment output went, so if your output is not ~/personal/output, please set OUT appropriately: | | OUT needs to point to where your alignment output went, so if your output is not ~/personal/output, please set OUT appropriately: |
| export OUT=~/personal/YOUR_OUTPUT_DIR | | export OUT=~/personal/YOUR_OUTPUT_DIR |
| + | After setting this, also do |
| + | mkdir -p $OUT/ancestry |
| | | |
| Verify that this does not give an error: | | Verify that this does not give an error: |
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| -m $HGDP/HGDP_938.site \ | | -m $HGDP/HGDP_938.site \ |
| -o $OUT/ancestry/$SAMPLE.laser \ | | -o $OUT/ancestry/$SAMPLE.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. |
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| | | |
| View the results: | | View the results: |
− | less -S $OUT/ancestry/Sample_37224.laser.1.SeqPC.coord | + | less -S $OUT/ancestry/${SAMPLE}.laser.2.SeqPC.coord |
| | | |
| == Visualizing Ancestry == | | == Visualizing Ancestry == |
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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}.laser.2.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}.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 & |