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SeqShop: Analysis of Structural Variation Practical, December 2014 (view source)

Revision as of 17:09, 17 December 2014

3,582 bytes added ,  17:09, 17 December 2014
→‎What does a real SV look like?
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Main Workshop wiki page: [[SeqShop: December 2014]]
 
Main Workshop wiki page: [[SeqShop: December 2014]]
   −
See the [[Media:Seqshop cnv partb 2014 06.pdf|introductory slides]] for an intro to this tutorial.
+
See [[Media:Seqshop cnv partb 2014 06.pdf|lecture slides]] for the lecture slides associated with this tutorial.
    
== Goals of This Session ==
 
== Goals of This Session ==
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== Setup in person at the SeqShop Workshop ==
 
== Setup in person at the SeqShop Workshop ==
 
''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" style="width:600px">
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<div class="mw-collapsible mw-collapsed" 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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* Setup an output directory
 
* Setup an output directory
 
** It will leave your output directory from the previous tutorial in tact.
 
** It will leave your output directory from the previous tutorial in tact.
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  source /home/mktrost/seqshop/setup.txt
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  source /net/seqshop-server/home/mktrost/seqshop/setup.txt
 
* You won't see any output after running <code>source</code>
 
* You won't see any output after running <code>source</code>
 
** It silently sets up your environment
 
** It silently sets up your environment
 
** If you want to view the detail of the setup, type
 
** If you want to view the detail of the setup, type
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  less /home/mktrost/seqshop/setup.txt
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  less /net/seqshop-server/home/mktrost/seqshop/setup.txt
 
and press 'q' to finish.
 
and press 'q' to finish.
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</div>
 
</div>
 
</div>
 
</div>
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== Setup when running on your own outside of the SeqShop Workshop ==
 
== Setup when running on your own outside of the SeqShop Workshop ==
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In addition, if one wants to genotype structural variants from other structural variant caller, there is a step available.
 
In addition, if one wants to genotype structural variants from other structural variant caller, there is a step available.
 
* Third-party Genotyping and Filtering step : Perform genotyping on the variant sites specified by an input VCF, and also perform variant filtering.
 
* Third-party Genotyping and Filtering step : Perform genotyping on the variant sites specified by an input VCF, and also perform variant filtering.
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 +
== Command Line Usage of GenomeSTRiP pipeline ==
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 +
To see how to use GenomeSTRiP pipeline, type
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perl $GC/bin/genomestrip.pl
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 +
<div class="mw-collapsible mw-collapsed">
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''View Results''
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<div class="mw-collapsible-content">
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ERROR: One of command options among --run-metadata, --run-discovery, --run-genotype, --run-thirdparty must be specified
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ERROR: Missing required option, outdir
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Usage:
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    /net/seqshop-server/home/mktrost/seqshop/gotcloud/bin/genomestrip.pl
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    [options]
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 +
    Help Options:
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      -help                Print out brief help message [OFF]
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      -man                Print the full documentation in man page style [OFF]
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 +
    Command options:
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      -run-metadata        Create metadata [OFF]
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      -run-discovery      Run variant discovery and filtering. Can run with --run-metadata together [OFF]
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      -run-genotype        Run genotyping - requires to finish run-metadata and run-discovery [OFF]
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      -run-thirdparty      Run genotyping and filtering of third-party sites [OFF]
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 +
    Options for input/output data:
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      -gotcloudroot|gcroot STRGotCloud Root Directory []
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      -conf STR            GotCloud configuration files []
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      -outdir STR          Override's conf file's OUT_DIR.  Used as the genomestrip output directory unless --out or GENOMESTRIP_OUT is set []
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      -list STR            BAM list file containing ID and BAM path []
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      -out STR            Output directory which stores subdirectories such as metadata/, discovery/, genotypes/, thirdparty/ unless overriden individually []
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      -metadata STR        Output directory to store --run-metadata results. Default is [OUT]/metadata/ []
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      -discovery STR      Output directory to store --run-discovery results. Default is [OUT]/discovery/ []
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      -genotype STR        Output directory to store --run-genotype results. Default is [OUT]/genotype/ []
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      -thirdparty STR      Output directory to store --run-thirdparty results. Default is [OUT]/thirdparty/ []
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    Advanced Options:
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      -tmp-dir STR        temporary directory to store temporary files. Default is [OUT]/tmp []
 +
      -gs-dir STR          GenomeSTRiP svtoolkit directory []
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      -param STR          GenomeSTRIP parameter file []
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      -ref STR            Reference FASTA file []
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      -mask STR            Reference mask FASTA file []
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      -ploidy-map STR      Ploidy map file []
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      -mosix-opt STR      MOSIX options []
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      -region STR          Region to focus on the variants []
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      -unit INT            Number of variants to be genotyped per parallel run [100]
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    Additional Inputs:
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      -in-vcf STR          Input site VCF files used for --run-genotype or --run-thirdparty. For --run-thirdparty, this argument is required. For --run-genotype, default is [OUT]/discovery/discovery.vcf []
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      -pass-only          Genotype only PASS-filtered variants, default is OFF [OFF]
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      -skip-rc            Skip precomputing read count [OFF]
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      -base-prefix STR    Prefix of all files []
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      -bam-prefix STR      Prefix of BAM files []
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      -ref-prefix STR      Prefix of Reference FASTA files []
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      -no-phonehome        Skip phone home functionality [OFF]
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      -make-base-name STR  Specifies the basename for the makefile []
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      -verbose            Specifies that additional details are to be printed out [OFF]
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      -dry-run            Perform a dry-run that only produces Makefile but not run it [OFF]
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      -numjobs INT        Number of jobs to concurrently run [1]
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      -autosomes          Perform analysis only on autosomes [OFF]
 +
</div></div>
    
== Running GotCloud/GenomeSTRiP Metadata Pipeline ==
 
== Running GotCloud/GenomeSTRiP Metadata Pipeline ==
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<div class="mw-collapsible-content" style="width:800px">
 
<div class="mw-collapsible-content" style="width:800px">
 
       7 COHERENCE;COVERAGE;DEPTH;DEPTHPVAL
 
       7 COHERENCE;COVERAGE;DEPTH;DEPTHPVAL
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     17 COHERENCE;COVERAGE;DEPTH;DEPTHPVAL;PAIRSPERSAMPLE
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     18 COHERENCE;COVERAGE;DEPTH;DEPTHPVAL;PAIRSPERSAMPLE
 
       3 COHERENCE;COVERAGE;DEPTH;PAIRSPERSAMPLE
 
       3 COHERENCE;COVERAGE;DEPTH;PAIRSPERSAMPLE
 
       2 COHERENCE;COVERAGE;DEPTHPVAL;PAIRSPERSAMPLE
 
       2 COHERENCE;COVERAGE;DEPTHPVAL;PAIRSPERSAMPLE
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       2 COVERAGE;DEPTH;PAIRSPERSAMPLE
 
       2 COVERAGE;DEPTH;PAIRSPERSAMPLE
 
       4 COVERAGE;DEPTHPVAL
 
       4 COVERAGE;DEPTHPVAL
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       5 COVERAGE;DEPTHPVAL;PAIRSPERSAMPLE
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       4 COVERAGE;DEPTHPVAL;PAIRSPERSAMPLE
 
       5 COVERAGE;PAIRSPERSAMPLE
 
       5 COVERAGE;PAIRSPERSAMPLE
 
</div>
 
</div>
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</div>
 
</div>
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== Starting SNP Call on your own Genome ==
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−
Go to [[SeqShop: Calling Your Own Genome, December 2014]] so we can run SNP calling overnight.
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== Return to Workshop Wiki Page ==
 +
Return to main workshop wiki page: [[SeqShop: December 2014]]
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12309...12432"

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