From Genome Analysis Wiki
Jump to navigationJump to search
179 bytes removed
, 10:23, 10 December 2014
Line 323: |
Line 323: |
| 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. | | * 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 ${GC}/bin/genomestrip.pl --run-genotype --metadata ${SS}/metadata --conf ${SS}/gotcloud.conf --numjobs 2 --base-prefix ${SS} --outdir ${OUT} |
− | * The added <code>--gcroot ${GC}</code> option directs the pipeline to tabix/bgzip programs found within gotcloud.
| |
| | | |
| This will take ~3 minutes to finish. | | This will take ~3 minutes to finish. |