Line 4: |
Line 4: |
| Set these values. If you used a different path for any of these, please update here. Also, be sure to specify your sample name instead of Sample_XXXXX | | Set these values. If you used a different path for any of these, please update here. Also, be sure to specify your sample name instead of Sample_XXXXX |
| | | |
− | source /home/chaolong/LASER-Tutorial/setup.txt | + | source /home/mktrost/seqshop-server/setup.txt |
− | export LASER=~/ancestry/LASER-2.01/
| |
− | export OUT=~/personal/output
| |
| export SAMPLE=Sample_XXXXX | | export SAMPLE=Sample_XXXXX |
− | mkdir $OUT/ancestry
| |
| | | |
| + | |
| + | 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 |
| + | |
| + | Verify that this does not give an error: |
| + | ls $OUT/bams/${SAMPLE}.recal.bam |
| | | |
| | | |
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Line 20: |
| | | |
| $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/hs37d5.fa -l $HGDP/HGDP_938.bed $OUT/bams/${SAMPLE}.recal.bam > $OUT/ancestry/${SAMPLE}.recal.pileup | | $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/hs37d5.fa -l $HGDP/HGDP_938.bed $OUT/bams/${SAMPLE}.recal.bam > $OUT/ancestry/${SAMPLE}.recal.pileup |
| + | |
| + | This step takes 5-6 minutes. |
| | | |
| === Step 2: pileup --> seq === | | === Step 2: pileup --> seq === |
| + | |
| python $LASER/pileup2seq/pileup2seq.py \ | | python $LASER/pileup2seq/pileup2seq.py \ |
| -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_37224.recal.pileup |
| + | |
| + | This step takes just a few seconds. |
| | | |
| === Estimate ancestry === | | === Estimate ancestry === |
| + | This step will take about 19 minutes. |
| + | |
| $LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s $OUT/ancestry/$SAMPLE.laser.seq -K 20 -k 4 -x 1 -y 3 -o $OUT/ancestry/$SAMPLE.laser.1 & | | $LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s $OUT/ancestry/$SAMPLE.laser.seq -K 20 -k 4 -x 1 -y 3 -o $OUT/ancestry/$SAMPLE.laser.1 & |
| + | |
| + | View the results: |
| + | less -S $OUT/ancestry/Sample_37224.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 |
| + | |
| + | Generate the plot: |
| + | Rscript plotHGDP.r $HGDP/HGDP_938.RefPC.coord $OUT/ancestry/Sample_37224.laser.1.SeqPC.coord |
| + | |
| + | Take a look: |
| + | evince Results_on_HGDP.pdf & |