Changes

From Genome Analysis Wiki
Jump to navigationJump to search

SeqShop: Variant Calling and Filtering for SNPs Practical, May 2015 (view source)

Revision as of 18:35, 19 August 2015

1,089 bytes removed ,  18:35, 19 August 2015
→‎Filtered VCF: since the uncompressed vcf isn't created, use zless on the compressed
Line 2: Line 2:  
Main Workshop wiki page: [[SeqShop: May 2015]]
 
Main Workshop wiki page: [[SeqShop: May 2015]]
   −
See the [[Media:Dec2014 SeqShop - GotCloud snpcall.pdf|introductory slides]] for an intro to this tutorial.
+
See the [[Media:May2015 SeqShop - GotCloud snpcall.pdf|introductory slides]] for an intro to this tutorial.
    
== Goals of This Session ==
 
== Goals of This Session ==
Line 11: Line 11:  
** How to evaluate the quality of SNP calls
 
** How to evaluate the quality of SNP calls
   −
== Setup in person at the SeqShop Workshop ==
+
== Setup ==
 
''This section is specifically for the SeqShop Workshop computers.''
 
''This section is specifically for the SeqShop Workshop computers.''
−
<div class="mw-collapsible mw-collapsed" style="width:600px">
+
<div class="mw-collapsible" style="width:600px">
 
''If you are not running during the SeqShop Workshop, please skip this section.''
 
''If you are not running during the SeqShop Workshop, please skip this section.''
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
−
  −
   
{{SeqShopLogin}}
 
{{SeqShopLogin}}
−
  −
=== Setup your run environment===
  −
This is the same setup you did for the previous tutorial, but you need to redo it each time you log in.
  −
  −
This will setup some environment variables to point you to
  −
* [[GotCloud]] program
  −
* Tutorial input files
  −
* Setup an output directory
  −
** It will leave your output directory from the previous tutorial in tact.
  −
source /net/seqshop-server/home/mktrost/seqshop/setup.txt
  −
* You won't see any output after running <code>source</code>
  −
** It silently sets up your environment
  −
** If you want to view the detail of the setup, type
  −
less /net/seqshop-server/home/mktrost/seqshop/setup.txt
  −
and press 'q' to finish.
  −
  −
<div class="mw-collapsible mw-collapsed" style="width:200px">
  −
View setup.txt
  −
<div class="mw-collapsible-content">
  −
[[File:setup.png|500px]]
  −
</div>
  −
</div>
   
</div>
 
</div>
 
</div>
 
</div>
   −
== Setup when running on your own outside of the SeqShop Workshop ==
+
=== Prerequisite Tutorials ===
−
''This section is specifically for running on your own outside of the SeqShop Workshop.''
  −
<div class="mw-collapsible" style="width:600px">
  −
''If you are running during the SeqShop Workshop, please skip this section.''
  −
<div class="mw-collapsible-content">
  −
 
   
This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]]
 
This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]]
    
{{SeqShopRemoteEnv}}
 
{{SeqShopRemoteEnv}}
−
</div>
  −
</div>
  −
      
== Examining GotCloud SnpCall Input files ==
 
== Examining GotCloud SnpCall Input files ==
Line 188: Line 156:     
Now that we have all of our input files, we need just a simple command to run:
 
Now that we have all of our input files, we need just a simple command to run:
−
* When running at home if you don't have 6 CPUs, reduce the --numjobs setting (it will take longer to run).
+
* When running at home if you don't have 8 CPUs, reduce the --numjobs setting (it will take longer to run).
−
  ${GC}/gotcloud snpcall --conf ${SS}/gotcloud.conf --numjobs 6 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
+
  ${GC}/gotcloud snpcall --conf ${SS}/gotcloud.conf --numjobs 8 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
 
* <code>${GC}/gotcloud</code> runs GotCloud
 
* <code>${GC}/gotcloud</code> runs GotCloud
 
* <code>snpcall</code> tells GotCloud you want to run the snpcall pipeline.
 
* <code>snpcall</code> tells GotCloud you want to run the snpcall pipeline.
Line 210: Line 178:  
</div>
 
</div>
 
</div>
 
</div>
−
This should take about 5-8 minutes to run.
+
This should take about 3-6 minutes to run.
 
* It should end with a line like: <code>Commands finished in 402 secs with no errors reported</code>
 
* It should end with a line like: <code>Commands finished in 402 secs with no errors reported</code>
   Line 276: Line 244:     
Let's look at the filtered sites file.
 
Let's look at the filtered sites file.
−
  less -S ${OUT}/vcfs/chr22/chr22.filtered.sites.vcf
+
  zless -S ${OUT}/vcfs/chr22/chr22.filtered.sites.vcf.gz
    
* Scroll down until you find some variants.
 
* Scroll down until you find some variants.
Line 369: Line 337:  
=== Running GotCloud Genotype Refinement ===
 
=== Running GotCloud Genotype Refinement ===
 
Since everything is setup, just run the following command (very similar to snpcall).
 
Since everything is setup, just run the following command (very similar to snpcall).
−
  ${GC}/gotcloud ldrefine --conf ${SS}/gotcloud.conf --numjobs 6 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
+
  ${GC}/gotcloud ldrefine --conf ${SS}/gotcloud.conf --numjobs 8 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
    
* Beagle will take about 1-3 minutes to complete
 
* Beagle will take about 1-3 minutes to complete
Line 444: Line 412:  
<li><code>1|1</code>; Homozygous Alt (C)</li>
 
<li><code>1|1</code>; Homozygous Alt (C)</li>
 
</ul>
 
</ul>
 +
Note the '|' instead of '/'.  The '|' indicates it is now phased.
 
</div>
 
</div>
 
</div>
 
</div>
Line 545: Line 514:     
== Return to Workshop Wiki Page ==
 
== Return to Workshop Wiki Page ==
−
Return to main workshop wiki page: [[SeqShop: December 2014]]
+
Return to main workshop wiki page: [[SeqShop: May 2015]]
Pjvh
61

edits

Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/13264...13676"

Navigation menu