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| ==Introduction== | | ==Introduction== |
− | See the [[Media:SeqShop - GotCloud snpcall.pdf|introductory slides]] for an intro to this tutorial.
| + | Main Workshop wiki page: [[SeqShop: December 2014]] |
| | | |
| + | See the [[Media:Dec2014 SeqShop - GotCloud snpcall.pdf|introductory slides]] for an intro to 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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| == Setup when running on your own outside of the SeqShop Workshop == | | == Setup when running on your own outside of the SeqShop Workshop == |
| ''This section is specifically for running on your own outside of the SeqShop Workshop.'' | | ''This section is specifically for running on your own outside of the SeqShop Workshop.'' |
− | <div class="mw-collapsible mw-collapsed" style="width:600px"> | + | <div class="mw-collapsible" style="width:600px"> |
| ''If you are running during the SeqShop Workshop, please skip this section.'' | | ''If you are running during the SeqShop Workshop, please skip this section.'' |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
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| | | |
| {{SeqShopRemoteEnv}} | | {{SeqShopRemoteEnv}} |
| + | </div> |
| + | </div> |
| + | |
| | | |
| == Examining GotCloud SnpCall Input files == | | == Examining GotCloud SnpCall Input files == |
− | === Sequnce Alignment Files: BAM Files === | + | === Sequence Alignment Files: BAM Files === |
| Per sample BAM files contain sequence reads that are mapped to positions in the genome. | | Per sample BAM files contain sequence reads that are mapped to positions in the genome. |
| | | |
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| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
| <ul> | | <ul> |
− | <li>/home/YourUserName/out/bams/HG00640.recal.bam</li> | + | <li>/net/seqshop-server/home/YourUserName/out/bams/HG00640.recal.bam</li> |
| [[File:BamindexNew.png|500px]] | | [[File:BamindexNew.png|500px]] |
| </div> | | </div> |
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| <li>That's ok, we will use the <code>--base_prefix ${SS}</code> command-line option to prefix the BAM paths</li> | | <li>That's ok, we will use the <code>--base_prefix ${SS}</code> command-line option to prefix the BAM paths</li> |
| <li>Alternatively, we could have set BAM_PREFIX in <code>gotcloud.conf</code> to the path to the BAMs | | <li>Alternatively, we could have set BAM_PREFIX in <code>gotcloud.conf</code> to the path to the BAMs |
− | <pre>BAM_PREFIX = /home/username/seqshop/example</pre> </li> | + | <pre>BAM_PREFIX = /net/seqshop-server/home/mktrost/seqshop/example</pre> </li> |
| <ul> | | <ul> |
| <li>NOTE: the conf file can't interpret ${SS} environment variables or '~', so you would have to specify the full path</li> | | <li>NOTE: the conf file can't interpret ${SS} environment variables or '~', so you would have to specify the full path</li> |
− | <li>We just used the command-line option for this tutorial since this path will vary by user.</li> | + | <li>We just used the command-line option for this tutorial since this path will vary by user when running outside the workshop.</li> |
| </ul> | | </ul> |
| </div> | | </div> |
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| | | |
| 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: |
− | ${GC}/gotcloud snpcall --conf ${SS}/gotcloud.conf --numjobs 4 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT} | + | * When running at home if you don't have 6 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 ${OUT} |
| * <code>${GC}/gotcloud</code> runs GotCloud | | * <code>${GC}/gotcloud</code> runs GotCloud |
− | * <code>align</code> tells GotCloud you want to run the alignment pipeline. | + | * <code>snpcall</code> tells GotCloud you want to run the snpcall pipeline. |
| * <code>--conf</code> tells GotCloud the name of the configuration file to use. | | * <code>--conf</code> tells GotCloud the name of the configuration file to use. |
| ** The configuration for this test was downloaded with the seqshop input files. | | ** The configuration for this test was downloaded with the seqshop input files. |
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| ** The Configuration file cannot read environment variables, so we need to tell GotCloud the path to the input files, ${SS} | | ** The Configuration file cannot read environment variables, so we need to tell GotCloud the path to the input files, ${SS} |
| ** Alternatively, gotcloud.conf could be updated to specify the full paths | | ** Alternatively, gotcloud.conf could be updated to specify the full paths |
− | * <code>--out_dir</code> tells GotCloud where to write the output. | + | * <code>--outdir</code> tells GotCloud where to write the output. |
| ** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line | | ** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line |
| | | |
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| </div> | | </div> |
| </div> | | </div> |
− | This should take about 5-7 minutes to run. | + | This should take about 5-8 minutes to run. |
− | * After about 4 minutes of running, GotCloud snpcall will output some text to the screen. Don't worry, that is expected and is just output from some of the intermediate tools.
| + | * 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 329 secs with no errors reported</code> | |
| | | |
| If you cancelled GotCloud part way through, just rerun your GotCloud command and it will pick up where it left off. | | If you cancelled GotCloud part way through, just rerun your GotCloud command and it will pick up where it left off. |
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| === 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 2 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT} | + | ${GC}/gotcloud ldrefine --conf ${SS}/gotcloud.conf --numjobs 6 --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 |
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| Let's get some information on the BEAGLE VCF: | | Let's get some information on the BEAGLE VCF: |
| | | |
− | perl ${GC}/scripts/bed-diff.pl --vcf1 ${SS}/ref22/1kg.omni.chr22.36Mb.vcf.gz --vcf2 ${OUT}/beagle/chr22/chr22.filtered.PASS.beagled.ALL.vcf.gz --out ${OUT}/bedDiff.beagle | + | perl ${GC}/scripts/bed-diff.pl --vcf1 ${SS}/ref22/1kg.omni.chr22.36Mb.vcf.gz --vcf2 ${OUT}/beagle/chr22/chr22.filtered.PASS.beagled.ALL.vcf.gz --out ${OUT}/diffs/bedDiff.beagle |
| | | |
| | | |
| Look at the results: | | Look at the results: |
− | more ${OUT}/bedDiff.beagle.summary | + | more ${OUT}/diffs/bedDiff.beagle.summary |
| | | |
| <div class="mw-collapsible mw-collapsed" style="width:400px"> | | <div class="mw-collapsible mw-collapsed" style="width:400px"> |
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| Now, let's see if it improved after running Thunder VCF: | | Now, let's see if it improved after running Thunder VCF: |
− | perl ${GC}/scripts/bed-diff.pl --vcf1 ${SS}/ref22/1kg.omni.chr22.36Mb.vcf.gz --vcf2 ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz --out ${OUT}/bedDiff.thunder | + | perl ${GC}/scripts/bed-diff.pl --vcf1 ${SS}/ref22/1kg.omni.chr22.36Mb.vcf.gz --vcf2 ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz --out ${OUT}/diffs/bedDiff.thunder |
| | | |
| Look at the results: | | Look at the results: |
− | more ${OUT}/bedDiff.thunder.summary | + | more ${OUT}/diffs/bedDiff.thunder.summary |
| | | |
| <div class="mw-collapsible mw-collapsed" style="width:400px"> | | <div class="mw-collapsible mw-collapsed" style="width:400px"> |
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| | | |
| Aren't you glad you didn't have to configure & run each one yourself? | | Aren't you glad you didn't have to configure & run each one yourself? |
| + | |
| + | |
| + | == Return to Workshop Wiki Page == |
| + | Return to main workshop wiki page: [[SeqShop: December 2014]] |