3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSeqShop: Variant Calling and Filtering for INDELs Practical, December 2014 (view source)
Revision as of 21:26, 7 December 2014
, 21:26, 7 December 2014→Running GotCloud Indel
== Running GotCloud Indel ==
== Running GotCloud Indel ==
${GC}/gotcloud indel --conf ${SS}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
${GC}/gotcloud indel --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>indel</code> tells GotCloud you want to run the indel calling pipeline.
* <code>indel</code> tells GotCloud you want to run the indel calling pipeline.
** 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
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.
== Examining GotCloud indel Ouptut ==
== Examining GotCloud indel Ouptut ==
