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− | <div class="mw-collapsible mw-collapsed" style="width:700px">
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− | '''Only if your snpcalling is still running, let Mary Kate know, expand, and follow these instructions'''
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− | <div class="mw-collapsible-content">
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− | * Detach from screen
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− | Ctrl-a d
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− | * Start new screen
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− | screen
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− | * Reset environment variables (replace SampleXX with your sample name)
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− | export SAMPLE=SampleXX
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− | source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
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− | * When you detach from screen and reattach, you will have multiple screen sessions
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− | ** The ancestry one will have today's date, the snpcall one will have an earlier date.
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− | *** Mary Kate can explain how to reattach to a specific session when we get there.
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− | </div>
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− | </div>
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− |
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− |
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− | '''Instructions for everyone: Setup LASER'''
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− | Source the LASER setup:
| + | '''Setup LASER''' |
− | source /net/seqshop-server/home/chaolong/LASER-Tutorial/setup.txt | + | export SSREF=/net/seqshop-server/home/mktrost/seqshop/singleSample/ref |
− | (SAMPLE & OUT were previously set in your screen session.) | + | export LASER=~/seqshop/output/ancestry/LASER-2.01 |
| + | (SAMPLE were previously set in your screen session.) |
| | | |
| After setting this, also do | | After setting this, also do |
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| === Step 1: bam --> pileup === | | === Step 1: bam --> pileup === |
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− | $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $OUT/bams/${SAMPLE}.recal.bam > $OUT/ancestry/${SAMPLE}.HGDP.pileup | + | $GC/bin/samtools mpileup -q 30 -Q 20 -f $SSREF/gotcloud.ref/hs37d5.fa -l $SSREF/HGDP/HGDP_938.bed $OUT/bams/${SAMPLE}.recal.bam > $OUT/ancestry/${SAMPLE}.HGDP.pileup |
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| This step takes ~1 hour for a genome sequenced at 17X. | | This step takes ~1 hour for a genome sequenced at 17X. |
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| 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 === |
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| python $LASER/pileup2seq/pileup2seq.py \ | | python $LASER/pileup2seq/pileup2seq.py \ |
− | -m $HGDP/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 |
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| This step will take about 5-6 minutes. | | This step will take about 5-6 minutes. |
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− | $LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/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: |
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| 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 |
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| Take a look: | | Take a look: |
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| 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 & |
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| 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: |
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| == Return to Calling your own Genome == | | == Return to Calling your own Genome == |
− | Go to [[SeqShop:_Calling_Your_Own_Genome,_December_2014#Reviewing_Indel_Results]] and pick up where we left off. | + | Go to [[SeqShop:_Calling_Your_Own_Genome,_May_2015#Reviewing_Indel_Results]] and pick up where we left off. |