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SeqShop: Calling Your Own Genome, May 2015

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== Tuesday - Start SNP Calling ==
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== Wednesday Thursday ==
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=== Checking if snpcall Completed ===
<div class="mw-collapsible-content">==== Logging Back in Resume screen to Check Jobs ====
;How do you log back into screen?
screen -r
This will resume an already running screen.
 
Your screen session still has your environment variables set, so you do not need to reset them.
 
Verify you got a "completed successfully" message.
How long did snpcall calling take? Look at the log message - time in seconds.
=== Detach From screen===
Detach from screen. We will resume it again later when we start SNPCall.
Ctrl-a d
 
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=== INDEL Tutorial ===
Now we are going to run the INDEL Practical
 
Please go to: [[SeqShop: Variant Calling and Filtering for INDELs Practical, May 2015]]
 
We will Start INDEL Calling after the practical.
 
 
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=== Start INDEL Calling ===
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==== Resume screen ====
 
;How do you log back into screen?
screen -r
This will resume an already running screen.
 
Your screen session still has your environment variables set, so you do not need to reset them.
==== List of BAMs ====
:<code>SampleXX SampleXX/output/bams/SampleXX.recal.bam</code>
* Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path).
 
==== GotCloud INDEL Configuration ====
cat ~/$SAMPLE/gotcloud.conf
Same as it looked yesterday the other day with no special Configuration settings for INDEL calling.
==== Running INDEL ====
Run GotCloud indel with 8 6 jobs running in parallel* Why 8? ** You want to run as many as you can.** 3 of you on the machine - 3*8 = 24 jobs will be running in parallel on that machine ${GC}/gotcloud indel --conf $SAMPLE/gotcloud.conf --numjobs 8 6 --outdir $OUT
* Only need the configuration, number of threads, and the output directory, rest is specified within the configuration.
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== Thursday ==
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=== Checking if INDEL Completed ===
==== Logging Back in to Check Jobs ====
 
;How do you log back into screen?
screen -r
This will resume an already running screen.
 
==== Checking Completion ====
 
Did you get a "completed successfully" message?
 
If yes, how long did INDEL calling take? Look at the log message - time in seconds.
 
If no, are you running on seqshop-server? If so, KILL it. ssh -X to one of the seqshop machines and run on there.
Ctrl-c
 
Detach from screen. We will resume it again later.
Ctrl-a d
 
=== Ancestry Tutorial ===
Now we are going to run the Ancestry Practical
 
Please go to: [[SeqShop: Estimates of Genetic Ancestry Practical, May 2015]]
 
 
==== Log Out ====
;Want to log out and leave your job running?
In the screen window, type:
Ctrl-a d
(Hold down Ctrl and type 'a', let go of both and type 'd')
* This will "detach" from your screen session while your alignment continues to run.
 
exit PuTTY
 
 
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