3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSeqShop: Variant Calling and Filtering for SNPs Practical, May 2015 (view source)
Revision as of 22:57, 18 May 2015
, 22:57, 18 May 2015→Run GotCloud SnpCall
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:
* When running at home if you don't have 6 CPUs, reduce the --numjobs setting (it will take longer to run).
* When running at home if you don't have 8 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}
${GC}/gotcloud snpcall --conf ${SS}/gotcloud.conf --numjobs 8 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
* <code>${GC}/gotcloud</code> runs GotCloud
* <code>${GC}/gotcloud</code> runs GotCloud
* <code>snpcall</code> tells GotCloud you want to run the snpcall pipeline.
* <code>snpcall</code> tells GotCloud you want to run the snpcall pipeline.
</div>
</div>
</div>
</div>
This should take about 5-8 minutes to run.
This should take about 3-6 minutes to run.
* 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 402 secs with no errors reported</code>
