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.
module spider elprep to find out what environment modules are available for this application.
- HPC_ELPREP_DIR - installation directory
- HPC_ELPREP_BIN - executable directory
If you publish research that uses elprep you have to cite it as follows: