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@jemten jemten released this 29 Jun 07:53
· 51 commits to master since this release
v12.0.0
31c2fec
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Learn about vigilant mode.
  • Set overlap requirement for merging two SVs to 0.8, down from the 0.95 default
  • Set overlap requirement for SV annotation to 0.6, up from 0.5
  • Update Tiddit to improve SV positioning
  • Increased memory allocation for salmon and picardtools_mergersamfiles (RNA)
  • New version of MegaFusion. A bug in the previous version prevented SVDB from writing the format and sample field in the vcf.
  • Remove the RSeQC read duplication analysis as it often fails.
  • Increased run time allocation for gatk_asereadcounter.
  • Increased the default required length for a trimmed rna read to be retained from 20 bp to 40 bp. Configurable via CLI or config.
  • Fixed a bug where gnomad SV version 2.0 instead of version 2.1 was used to annotate SVs
  • One-pass instead of two-pass mapping with STAR-Fusion, as recommended for STAR-Fusion 1.12
  • Bump max run time for retroseq to 15 hours.

Tools

  • Arriba 2.3.0 -> 2.4.0
  • DeepVariant 1.4.0 -> 1.5.0
  • FastQC: 0.11.9 -> 0.12.1
  • GATK: 4.2.6.1 -> 4.4.0.0
  • Gffcompare 0.11.2 -> 0.12.6
  • Htslib 1.15.1 -> 1.16
  • MegaFusion 66a3a80 -> d3feacf
  • Picard 2.27.2 -> 2.27.5
  • STAR-Fusion 1.11.0 -> 1.12.0
  • SVDB: 2.7.0 -> 2.8.2
  • Tiddit 3.3.2 -> 3.6.0

Databases

clinvar: 20220829 -> 20230508
loqusdb snapshot: 20230208 -> 20230512
hmtvar: oct2022

Assets 2
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