Difference between revisions of "SMRT-SV"
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 21:24, 6 December 2019
Description
SMRT-SV calls structural variants (SVs) using long reads (PacBio RS II or Sequel). The input is an FOFN file that lists each input file (BAX H5 or BAM) and a genome reference. Reads are aligned to the reference and local assemblies are done in kilobase-scale overlapping windows across the genome. Assemblies are aligned back to the reference, and structural variants are called from them.
Because of this approach, SMRT-SV yields both SV calls and contigs containing the SV with know breakpoints on the contig. These data feed into powerful analysis tools that use the reference and the contigs, such as the SMRT-SV genotyper, which is also included in this package.
Environment Modules
Run module spider smrtsv2 to find out what environment modules are available for this application.
System Variables
- HPC_SMRTSV2_DIR - installation directory