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

Revision as of 11:22, 20 May 2015

1,919 bytes removed ,  11:22, 20 May 2015
→‎Return to Workshop Wiki Page
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Main Workshop wiki page: [[SeqShop: May 2015]]
 
Main Workshop wiki page: [[SeqShop: May 2015]]
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See the [[Media:Dec2014 SeqShop - GotCloud indel.pdf|introductory slides]] for an intro to this tutorial.
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See the [[Media:May2015 SeqShop - GotCloud indel.pdf|introductory slides]] for an intro to this tutorial.
    
== Goals of This Session ==
 
== Goals of This Session ==
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** How to evaluate the quality of INDEL calls
 
** How to evaluate the quality of INDEL calls
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== Setup in person at the SeqShop Workshop ==
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== Setup ==
 
''This section is specifically for the SeqShop Workshop computers.''
 
''This section is specifically for the SeqShop Workshop computers.''
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<div class="mw-collapsible mw-collapsed" style="width:600px">
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<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">
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{{SeqShopLogin}}
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{{SeqShopLoginA}}
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=== Setup your run environment===
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This is the same setup you did for the previous tutorial, but you need to redo it each time you log in.
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This will setup some environment variables to point you to
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* [[GotCloud]] program
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* Tutorial input files
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* Setup an output directory
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** It will leave your output directory from the previous tutorial in tact.
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source /net/seqshop-server/home/mktrost/seqshop/setup.txt
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* You won't see any output after running <code>source</code>
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** It silently sets up your environment
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** If you want to view the detail of the setup, type
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less /net/seqshop-server/home/mktrost/seqshop/setup.txt
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and press 'q' to finish.
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<div class="mw-collapsible mw-collapsed" style="width:200px">
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View setup.txt
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<div class="mw-collapsible-content">
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[[File:setup.png|500px]]
   
</div>
 
</div>
 
</div>
 
</div>
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</div>
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</div>
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== Setup when running on your own outside of the SeqShop Workshop ==
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''This section is specifically for running on your own outside of the SeqShop Workshop.''
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<div class="mw-collapsible" style="width:600px">
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''If you are running during the SeqShop Workshop, please skip this section.''
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<div class="mw-collapsible-content">
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=== Prerequisite Tutorials ===
 
This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical, May 2015|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, May 2015|Alignment Tutorial]]
    
It also uses the bam.list file created in the SnpCall Tutorial.  If you have not yet run that tutorial, please follow the directions at: [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical, May 2015#GotCloud_BAM_List_File|GotCloud BAM List File]]
 
It also uses the bam.list file created in the SnpCall Tutorial.  If you have not yet run that tutorial, please follow the directions at: [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical, May 2015#GotCloud_BAM_List_File|GotCloud BAM List File]]
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{{SeqShopRemoteEnv}}
 
{{SeqShopRemoteEnv}}
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</div>
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</div>
      
== Examining GotCloud Indel Input files ==
 
== Examining GotCloud Indel Input files ==
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== Running GotCloud Indel ==
 
== Running GotCloud Indel ==
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  ${GC}/gotcloud indel --conf ${SS}/gotcloud.conf --numjobs 6 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
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  ${GC}/gotcloud indel --conf ${SS}/gotcloud.conf --numjobs 3 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
 
* <code>${GC}/gotcloud</code> runs GotCloud
 
* <code>${GC}/gotcloud</code> runs GotCloud
 
* <code>indel</code> tells GotCloud you want to run the indel calling pipeline.
 
* <code>indel</code> tells GotCloud you want to run the indel calling pipeline.
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It is usually useful to examine the call sets against known data sets for the passed variants.
 
It is usually useful to examine the call sets against known data sets for the passed variants.
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<div class="mw-collapsible mw-collapsed" style="width:500px">
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''Command to use at SeqShop Workshop:''
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Currently indel.reference.txt needs absolute paths to the reference files, so update indel.reference.txt to point to the reference files.
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<div class="mw-collapsible-content">
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${GC}/bin/vt profile_indels -g ${SS}/ref22/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"
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</div>
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</div>
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<div class="mw-collapsible" style="width:500px">
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''Commands outside of SeqShop Workshop:''
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<div class="mw-collapsible-content">
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Outside the workshop, you need to update indel.reference.txt to point to the reference files.
   
  cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt
 
  cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt
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  ${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt  -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"
 
  ${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt  -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"
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</div>
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</div>
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We perform the same analysis for the failed variants again, the relatively low overlap with known data sets imply a reasonable tradeoff in sensitivity and specificity.
 
We perform the same analysis for the failed variants again, the relatively low overlap with known data sets imply a reasonable tradeoff in sensitivity and specificity.
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<div class="mw-collapsible mw-collapsed" style="width:500px">
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''Command to use at SeqShop Workshop:''
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<div class="mw-collapsible-content">
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  ${GC}/bin/vt profile_indels -g ${SS}/ref22/indel.reference.txt  -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f  "~PASS"
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</div>
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</div>
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<div class="mw-collapsible" style="width:500px">
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''Command outside of SeqShop Workshop:''
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<div class="mw-collapsible-content">
   
   ${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt  -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f  "~PASS"
 
   ${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt  -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f  "~PASS"
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</div>
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</div>
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UMICH's algorithm for normalization has been adopted by Petr Danecek in bcftools and is also used in GKNO.
 
UMICH's algorithm for normalization has been adopted by Petr Danecek in bcftools and is also used in GKNO.
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== FEEDBACK! ==
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Please provide feedback on today:
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https://docs.google.com/forms/d/1xLrrEJ3XeZjxR_e5Fo-OTKHQvUFQLgX8MYwLZtxroig/viewform
    
== Return to Workshop Wiki Page ==
 
== Return to Workshop Wiki Page ==
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Return to main workshop wiki page: [[SeqShop: December 2014]]
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Return to main workshop wiki page: [[SeqShop: May 2015]]
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/13272...13389"

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