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Run GotCloud SnpCall
Now that we have all of our input files, we need just a simple command to run:
${GC}/gotcloud snpcall --conf ${GCIN}/inputs/gotcloud.conf --numjobs 4 --region 22:36000000-37000000
* --numjobs tells GotCloud how many jobs to run in parallel
** Depends on your system
* --region 22:36000000-37000000
** The sample files are just a small region of chromosome 22, so to save time, we tell Gotcloud GotCloud to ignore the other regions
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Curious if it started running properly? Check out this screenshot:
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This should take about 5 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>TBDCommands finished in 289 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.

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