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Old 10-22-2018, 02:51 AM   #1
costanza
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Location: Belgium

Join Date: Oct 2018
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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 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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File Type: pdf elprep4.0-release-notes.pdf (70.6 KB, 1 views)
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