[Announcement] elPrep v4.0.0 released

[costanza]

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.

[costanza]

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.