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Old 10-22-2018, 02:51 AM   #1
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Default [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

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

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 for a publication on a previous version of elPrep.
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File Type: pdf elprep4.0-release-notes.pdf (70.6 KB, 4 views)
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Old 12-12-2018, 05:15 AM   #2
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We have now published a preprint of an upcoming paper about elPrep 4.0.0 on bioaRxiv at with more details.
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