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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.'' |
− | <div class="mw-collapsible" style="width:600px"> | + | <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. |
− | source /home/mktrost/seqshop/setup.txt | + | 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 |
− | less /home/mktrost/seqshop/setup.txt | + | 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> |
− |
| |
| | | |
| == 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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| perl $GC/bin/genomestrip.pl | | perl $GC/bin/genomestrip.pl |
| | | |
| + | <div class="mw-collapsible mw-collapsed"> |
| + | ''View Results'' |
| + | <div class="mw-collapsible-content"> |
| ERROR: One of command options among --run-metadata, --run-discovery, --run-genotype, --run-thirdparty must be specified | | ERROR: One of command options among --run-metadata, --run-discovery, --run-genotype, --run-thirdparty must be specified |
| ERROR: Missing required option, outdir | | ERROR: Missing required option, outdir |
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| /net/seqshop-server/home/mktrost/seqshop/gotcloud/bin/genomestrip.pl | | /net/seqshop-server/home/mktrost/seqshop/gotcloud/bin/genomestrip.pl |
| [options] | | [options] |
− | | + | |
| Help Options: | | Help Options: |
| -help Print out brief help message [OFF] | | -help Print out brief help message [OFF] |
| -man Print the full documentation in man page style [OFF] | | -man Print the full documentation in man page style [OFF] |
− | | + | |
| Command options: | | Command options: |
| -run-metadata Create metadata [OFF] | | -run-metadata Create metadata [OFF] |
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| -run-genotype Run genotyping - requires to finish run-metadata and run-discovery [OFF] | | -run-genotype Run genotyping - requires to finish run-metadata and run-discovery [OFF] |
| -run-thirdparty Run genotyping and filtering of third-party sites [OFF] | | -run-thirdparty Run genotyping and filtering of third-party sites [OFF] |
− | | + | |
| Options for input/output data: | | Options for input/output data: |
| -gotcloudroot|gcroot STRGotCloud Root Directory [] | | -gotcloudroot|gcroot STRGotCloud Root Directory [] |
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| -genotype STR Output directory to store --run-genotype results. Default is [OUT]/genotype/ [] | | -genotype STR Output directory to store --run-genotype results. Default is [OUT]/genotype/ [] |
| -thirdparty STR Output directory to store --run-thirdparty results. Default is [OUT]/thirdparty/ [] | | -thirdparty STR Output directory to store --run-thirdparty results. Default is [OUT]/thirdparty/ [] |
− | | + | |
| Advanced Options: | | Advanced Options: |
| -tmp-dir STR temporary directory to store temporary files. Default is [OUT]/tmp [] | | -tmp-dir STR temporary directory to store temporary files. Default is [OUT]/tmp [] |
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| -region STR Region to focus on the variants [] | | -region STR Region to focus on the variants [] |
| -unit INT Number of variants to be genotyped per parallel run [100] | | -unit INT Number of variants to be genotyped per parallel run [100] |
− | | + | |
| Additional Inputs: | | Additional Inputs: |
| -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 [] | | -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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| -numjobs INT Number of jobs to concurrently run [1] | | -numjobs INT Number of jobs to concurrently run [1] |
| -autosomes Perform analysis only on autosomes [OFF] | | -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 |
− | 17 COHERENCE;COVERAGE;DEPTH;DEPTHPVAL;PAIRSPERSAMPLE | + | 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 |
− | 5 COVERAGE;DEPTHPVAL;PAIRSPERSAMPLE | + | 4 COVERAGE;DEPTHPVAL;PAIRSPERSAMPLE |
| 5 COVERAGE;PAIRSPERSAMPLE | | 5 COVERAGE;PAIRSPERSAMPLE |
| </div> | | </div> |
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| </div> | | </div> |
| | | |
− | == Starting SNP Call on your own Genome == | + | |
− | Go to [[SeqShop: Calling Your Own Genome, December 2014]] so we can run SNP calling overnight.
| + | == Return to Workshop Wiki Page == |
| + | Return to main workshop wiki page: [[SeqShop: December 2014]] |