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We have now published a preprint of an upcoming paper about elPrep 4.0.0 on bioaRxiv at https://doi.org/10.1101/492249 with more details. -
[Announcement] elPrep v4.0.0 released
We are happy to announce the release of elPrep v4.0.0. elPrep is an open-source, drop-in replacement tool for GATK4/Picard/SAMtools for preparing SAM/BAM files for variant calling that produces identical results, while greatly improving computational performance. See https://github.com/exascience/elprep
elPrep v4.0.0 introduces multiple new features allowing us to process the preparation steps defined by the GATK Best Practices for variant calling.
- added base quality score recalibration (BQSR, ApplyBQSR)
- added optical duplicate marking
- added MultiQC-compatible metrics
- support for SAM File Format version 1.6
- native support for BAM/BGZF files
- support for FASTA and VCF files
- support for elPrep-specific elsites and elfasta formats for improved performance
- split/filter/merge (sfm) now implemented in Go instead of Python
- added --log-path option to all tools
- various API and performance improvements
- changed license to the GNU Affero General Public License version 3 as published by the Free Software Foundation, with Additional Terms
- updated demos at https://github.com/ExaScience/elprep/tree/master/demo
Our benchmarks show that elPrep v4.0.0 executes the sort/deduplicate/recalibrate and apply-BQSR-pipeline from the GATK Best Practices up to 12x faster on WES data and 7.5x faster on WGS data, while using similar or fewer compute resources than Picard/GATK4.
See https://doi.org/10.1371/journal.pone.0132868 for a publication on a previous version of elPrep.
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