IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0244471.html
   My bibliography  Save this article

Multithreaded variant calling in elPrep 5

Author

Listed:
  • Charlotte Herzeel
  • Pascal Costanza
  • Dries Decap
  • Jan Fostier
  • Roel Wuyts
  • Wilfried Verachtert

Abstract

We present elPrep 5, which updates the elPrep framework for processing sequencing alignment/map files with variant calling. elPrep 5 can now execute the full pipeline described by the GATK Best Practices for variant calling, which consists of PCR and optical duplicate marking, sorting by coordinate order, base quality score recalibration, and variant calling using the haplotype caller algorithm. elPrep 5 produces identical BAM and VCF output as GATK4 while significantly reducing the runtime by parallelizing and merging the execution of the pipeline steps. Our benchmarks show that elPrep 5 speeds up the runtime of the variant calling pipeline by a factor 8-16x on both whole-exome and whole-genome data while using the same hardware resources as GATK4. This makes elPrep 5 a suitable drop-in replacement for GATK4 when faster execution times are needed.

Suggested Citation

  • Charlotte Herzeel & Pascal Costanza & Dries Decap & Jan Fostier & Roel Wuyts & Wilfried Verachtert, 2021. "Multithreaded variant calling in elPrep 5," PLOS ONE, Public Library of Science, vol. 16(2), pages 1-13, February.
    • Handle: RePEc:plo:pone00:0244471
    DOI: 10.1371/journal.pone.0244471
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244471
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0244471&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0244471?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Charlotte Herzeel & Pascal Costanza & Dries Decap & Jan Fostier & Wilfried Verachtert, 2019. "elPrep 4: A multithreaded framework for sequence analysis," PLOS ONE, Public Library of Science, vol. 14(2), pages 1-16, February.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.

      More about this item

      Statistics

      Access and download statistics

      Corrections

      All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0244471. See general information about how to correct material in RePEc.

      If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

      If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

      If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

      For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

      Please note that corrections may take a couple of weeks to filter through the various RePEc services.

      IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.