From Genome Analysis Wiki
Jump to navigationJump to search
584 bytes added
, 14:06, 17 October 2014
Line 81: |
Line 81: |
| #:<pre>cat output/vcfs/chr22/chr22.filtered.sites.vcf.summary</pre> | | #:<pre>cat output/vcfs/chr22/chr22.filtered.sites.vcf.summary</pre> |
| #:[[File::screenshot]] | | #:[[File::screenshot]] |
| + | |
| + | |
| + | === Run GotCloud Indel === |
| + | Now that we have examined the instance files, run GotCloud indel |
| + | # <pre>gotcloud indel --conf example/test.conf --outdir output --numjobs 8</pre> |
| + | #* The ubuntu user is setup to have the gotcloud program and tools in its path, so you can just type the program name and it will be found |
| + | #: [[File:RunIndel.png|700px]] |
| + | #:* This will take a few minutes to run. |
| + | #:* GotCloud first generates a makefile, and then runs the makefile |
| + | # When complete, GotCloud indel will indicate success/failure |
| + | #:[[File:IndelSuccess.png|700px]] |
| + | |
| + | ==== Examining Indel Output ==== |