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elprep website  

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


If you publish research that uses elprep you have to cite it as follows:

Herzeel C, Costanza P, Decap D, Fostier J, Verachtert W (2019) elPrep 4: A multithreaded framework for sequence analysis. PLoS ONE 14(2): e0209523. https://doi.org/10.1371/journal.pone.0209523