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SeqShop: Calling Your Own Genome, December 2014 (view source)

Revision as of 19:25, 9 December 2014

1,656 bytes added ,  19:25, 9 December 2014
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</div>
 
</div>
   −
== Setup ==
+
<div class="mw-collapsible mw-collapsed" style="width:500px">
−
The snpcall pipeline will run overnight, but you'll want to log out.
+
== Tuesday - Start INDEL Calling ==
 +
<div class="mw-collapsible-content">
 +
=== Setup ===
 +
The indel & snpcall pipelines will run overnight, but you'll want to log out.
 
; How do I leave something running on the server even if I log out?
 
; How do I leave something running on the server even if I log out?
 
: One solution is screen!
 
: One solution is screen!
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As it says, press <code>Space</code> or <code>Return</code>.
 
As it says, press <code>Space</code> or <code>Return</code>.
 
* It should now look basically the same as your normal command line.
 
* It should now look basically the same as your normal command line.
−
  −
; Scrolling problems when using screen?
  −
: If you want to scroll and screen doesn't scroll like you normally would?
  −
:* Type Ctrl-a Esc and you should be able to scroll up with your mouse wheel
  −
:** Or at least that is what I do from my Linux machine - (sorry I'm typing this up/testing these commands from Linux and not windows, so can't test it out)
  −
      
Set these values.  Also, be sure to specify your sample name instead of SampleXX
 
Set these values.  Also, be sure to specify your sample name instead of SampleXX
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:<code>export OUT=~/$SAMPLE/output</code>
 
:<code>export OUT=~/$SAMPLE/output</code>
   −
<div class="mw-collapsible" style="width:500px">
  −
  −
== SnpCall Step 1 (Day 1): Start SnpCall ==
  −
<div class="mw-collapsible-content">
   
=== List of BAMs ===
 
=== List of BAMs ===
 
The list of BAMs has already been created (just 1 BAM, your sample).
 
The list of BAMs has already been created (just 1 BAM, your sample).
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* Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path).
 
* Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path).
   −
=== Configuring SnpCall ===
+
=== Configuring Indel ===
−
 
+
No special Configuration settings for Indel calling
 
  cat ~/$SAMPLE/gotcloud.conf
 
  cat ~/$SAMPLE/gotcloud.conf
   Line 79: Line 72:  
</pre>
 
</pre>
   −
==== Configuration Updates ====
+
=== Running Indel Calling ===
−
In order to complete SnpCall overnight, we are going to tell GotCloud to only call SNPs for the EXOME regions.
+
Run GotCloud indel with 6 jobs running in parallel
−
 
  −
Edit 
  −
nedit $SAMPLE/gotcloud.conf&
  −
* Or you can use <code>vi</code> or <code>emacs</code> or your favorite editor
  −
 
  −
Specify the target region:
  −
UNIFORM_TARGET_BED = /net/seqshop-server/home/mktrost/seqshop/singleSample/20130108.exome.targets.bed
  −
* See [http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Pipeline#Targeted.2FExome_Sequencing_Settings|Targeted/Exome Sequencing Settings] for more information on the GotCloud configuration settings for running Targeted/Exome runs.
  −
 
  −
=== Running SnpCall ===
  −
Run GotCloud snpcall with 6 jobs running in parallel
   
* Why 6?   
 
* Why 6?   
 
** You want to run as many as you can.
 
** You want to run as many as you can.
 
** 5 of you on the machine - 5*6 = 30 jobs will be running in parallel on that machine
 
** 5 of you on the machine - 5*6 = 30 jobs will be running in parallel on that machine
−
  ${GC}/gotcloud snpcall --conf $SAMPLE/gotcloud.conf --numjobs 6
+
  ${GC}/gotcloud indel --conf $SAMPLE/gotcloud.conf --numjobs 6
 
* Only need the configuration & number of threads, rest is specified within the configuration.
 
* Only need the configuration & number of threads, rest is specified within the configuration.
   Line 116: Line 98:     
https://docs.google.com/forms/d/1n8xYxvsOq-HsabpDfGcHvwD84BYIRDx8_b-H5N3d-D8/viewform
 
https://docs.google.com/forms/d/1n8xYxvsOq-HsabpDfGcHvwD84BYIRDx8_b-H5N3d-D8/viewform
−
   
</div>
 
</div>
 
</div>
 
</div>
    
<div class="mw-collapsible" style="width:500px">
 
<div class="mw-collapsible" style="width:500px">
−
== SnpCall Step 2 (Day 2): Checking SnpCall ==
+
== Wednesday Checking if INDEL Completed ==
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
 
=== Logging Back in to Check Jobs ===
 
=== Logging Back in to Check Jobs ===
   −
;How do you log back into screen tomorrow?
+
;How do you log back into screen?
 
  screen -r
 
  screen -r
 
This will resume an already running screen.
 
This will resume an already running screen.
 +
 +
Verify you got a "completed successfully" message.
 +
 +
How long did INDEL calling take?  Look at the log message - time in seconds.
 +
 +
Detach from screen.  We will resume it again later when we start SNPCall.
 +
Ctrl-a d
    
</div>
 
</div>
 
</div>
 
</div>
 +
 +
== Wednesday - Structural Variation Tutorial ==
 +
Now we are going to run the Structural Variation Practical
 +
 +
Please go to: [[SeqShop: Analysis of Structural Variation Practical, December 2014]]
 +
 +
We will Start SNP Calling after the practical.
    
<div class="mw-collapsible" style="width:500px">
 
<div class="mw-collapsible" style="width:500px">
−
== Indel Step 1 (Day 1): Start Indel Calling ==
+
== Wednesday - Start SNP Calling ==
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
 +
=== Setup ===
 +
The indel & snpcall pipelines will run overnight, but you'll want to log out.
 +
; How do I leave something running on the server even if I log out?
 +
: One solution is screen!
 +
 +
; How do I use screen?
 +
: Before running your command, you need to start screen:
 +
: <pre>screen</pre>
 +
 +
[[File:Screen.png]]
 +
 +
As it says, press <code>Space</code> or <code>Return</code>.
 +
* It should now look basically the same as your normal command line.
 +
 +
Set these values.  Also, be sure to specify your sample name instead of SampleXX
 +
export SAMPLE=SampleXX
 +
source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
 +
 +
See the settings you just used:
 +
cat /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
 +
Shows you:
 +
:<code>export GC=/net/seqshop-server/home/mktrost/seqshop/gotcloud</code>
 +
:<code>export SS=/net/seqshop-server/home/mktrost/seqshop/singleSample</code>
 +
:<code>export OUT=~/$SAMPLE/output</code>
 +
 
=== List of BAMs ===
 
=== List of BAMs ===
 
The list of BAMs has already been created (just 1 BAM, your sample).
 
The list of BAMs has already been created (just 1 BAM, your sample).
Line 144: Line 164:  
* Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path).
 
* Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path).
   −
=== Configuring Indel ===
+
=== Configuring SnpCall ===
−
No special Configuration settings for Indel calling
+
 
 
  cat ~/$SAMPLE/gotcloud.conf
 
  cat ~/$SAMPLE/gotcloud.conf
   Line 172: Line 192:  
</pre>
 
</pre>
   −
=== Running Indel Calling ===
+
==== Configuration Updates ====
−
Run GotCloud indel with 6 jobs running in parallel
+
In order to complete SnpCall overnight, we are going to tell GotCloud to only call SNPs for the EXOME regions.
 +
 
 +
Edit 
 +
nedit $SAMPLE/gotcloud.conf&
 +
* Or you can use <code>vi</code> or <code>emacs</code> or your favorite editor
 +
 
 +
Specify the target region:
 +
UNIFORM_TARGET_BED = /net/seqshop-server/home/mktrost/seqshop/singleSample/20130108.exome.targets.bed
 +
* See [http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Pipeline#Targeted.2FExome_Sequencing_Settings|Targeted/Exome Sequencing Settings] for more information on the GotCloud configuration settings for running Targeted/Exome runs.
 +
 
 +
=== Running SnpCall ===
 +
Run GotCloud snpcall with 6 jobs running in parallel
 
* Why 6?   
 
* Why 6?   
 
** You want to run as many as you can.
 
** You want to run as many as you can.
 
** 5 of you on the machine - 5*6 = 30 jobs will be running in parallel on that machine
 
** 5 of you on the machine - 5*6 = 30 jobs will be running in parallel on that machine
−
  ${GC}/gotcloud indel --conf $SAMPLE/gotcloud.conf --numjobs 6
+
  ${GC}/gotcloud snpcall --conf $SAMPLE/gotcloud.conf --numjobs 6
 
* Only need the configuration & number of threads, rest is specified within the configuration.
 
* Only need the configuration & number of threads, rest is specified within the configuration.
   Line 194: Line 225:  
exit PuTTY
 
exit PuTTY
   −
=== Tuesday FEEDBACK! ===
+
=== Wednesday FEEDBACK! ===
 
Please provide feedback on the lectures/tutorials from today:  
 
Please provide feedback on the lectures/tutorials from today:  
   −
https://docs.google.com/forms/d/1n8xYxvsOq-HsabpDfGcHvwD84BYIRDx8_b-H5N3d-D8/viewform
+
https://docs.google.com/a/umich.edu/forms/d/1CCHL9ODPsw4jX4hj0kGo6AMHwT4Gam0IpKNRnIR9yMk/viewform
 +
 
 +
</div>
 +
</div>
 +
 
 +
<div class="mw-collapsible mw-collapsed" style="width:500px">
 +
== Thursday Checking if SnpCall Completed ==
 +
<div class="mw-collapsible-content">
 +
=== 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 SNP calling take?  Look at the log message - time in seconds.
 +
 
 +
If no, KILL it.  We will start it back running again after the tutorial today.
 +
 
 +
Detach from screen.  We will resume it again later when we restart SNPCall (if necessary).
 +
Ctrl-a d
 +
 
 
</div>
 
</div>
 
</div>
 
</div>
   −
<div class="mw-collapsible" style="width:500px">
+
 
−
== Indel Step 2 (Day 2): Checking Indel ==
+
 
 +
<div class="mw-collapsible mw-collapsed" style="width:500px">
 +
== Friday: Reviewing Indel Results ==
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
 
=== Logging Back in to Check Jobs ===
 
=== Logging Back in to Check Jobs ===
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12281"

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