Difference between revisions of "ElPrep"
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(Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|elprep}} |{{#vardefine:url|https://github.com/ExaScience/elprep}} <!--CONFIG...") |
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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 |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
<!--Configuration--> | <!--Configuration--> | ||
Latest revision as of 21:20, 6 December 2019
Description
elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4, and was extensively tested with different pipelines for variant analysis with GATK. The key advantage of elPrep is that it only performs a single-pass to process a .sam/.bam file, independent of the number of processing steps that need to be applied in a particular pipeline, greatly improving runtime performance.
Environment Modules
Run module spider elprep to find out what environment modules are available for this application.
System Variables
- HPC_ELPREP_DIR - installation directory
- HPC_ELPREP_BIN - executable directory
Citation
If you publish research that uses elprep you have to cite it as follows: