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Revision as of 11:14, 11 July 2014
, 11:14, 11 July 2014→Running GotCloud/GenomeSTRiP Genotyping Pipeline
The discovery pipeline only performs discovery of variant sites with filtering. You will need to iterate BAMs again to perform genotyping.
The discovery pipeline only performs discovery of variant sites with filtering. You will need to iterate BAMs again to perform genotyping.
* If running on a small machine, you may want to reduce <code>--numjobs</code> from 4 to 1.
time perl ${SS}/svtoolkit/bin/genomestrip.pl -run-genotype --metadata ${SS}/svtoolkit/metadata --conf ${SS}/gotcloud.conf --numjobs 4 --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT} --gcroot ${GC}
time perl ${SS}/svtoolkit/bin/genomestrip.pl -run-genotype --metadata ${SS}/svtoolkit/metadata --conf ${SS}/gotcloud.conf --numjobs 4 --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT} --gcroot ${GC}
* The added <code>--gcroot ${GC}</code> option directs the pipeline to tabix/bgzip programs found within gotcloud.
* The added <code>--gcroot ${GC}</code> option directs the pipeline to tabix/bgzip programs found within gotcloud.
