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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 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> | | </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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| | | |
| 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]] |