There is a newer version of the record available.

Published February 28, 2019 | Version 2.3
Software Open

SciLifeLab/Sarek: Äpar

Authors/Creators

  • 1. @SciLifeLab | Karolinska Institutet
  • 2. SciLifeLab
  • 3. @qbicsoftware
  • 4. Science for Life Laboratory
  • 5. Comparative Bioinformatics, CRG
  • 6. NBIS
  • 7. Rally Software

Description

  • mapping step can now map BAM files too
  • Improve ASCAT
  • Improve AWS Batch configuration
  • Improve bamQC
  • Improve VEP
  • Run Sarek with conda
  • Use SnpEff and VEP cache
  • Improve usage of targetBED params
  • Improve targeted for Manta
  • Multiple patients TSV file
  • Update VEP from 95.1 to 95.2
  • Strelka Best Practices output is now prefixed with StrelkaBP_
  • VCFs and Annotated VCFs are now ordered by Patient, then tools

Files

SciLifeLab/Sarek-2.3.zip

Files (13.4 MB)

Name Size Download all
md5:eaf014c625b18f88b26309075d689185
13.4 MB Preview Download

Additional details

Related works

Is supplement to
https://github.com/SciLifeLab/Sarek/tree/2.3 (URL)