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11.1.0

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@jemten jemten released this 14 Dec 08:00
· 165 commits to master since this release
v11.1.0
67561a6
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Learn about vigilant mode.
  • Save raw files from ExpansionHunter
  • Run UPD and subsequently chromograph on unaffected children
  • Annotate SV variants with the caller that reported the variant
  • Produce files for CNV analysis in Gens
  • Updated SO terms for new version of VEP
  • ExACpLI -> pLI, see vep issue 108
  • Use REVEL_score rather than REVEL_rankscore for the ranking algorithm
  • Use BWA-mem2 instead of BWA mem for mapping
  • Set default annotation overlap for structural variants to 0.5 (previously 0.8), due to change in TIDDIT
  • Turn on Stringtie and gffcompare by default
  • Run varg on research vcf
  • Increase max for coverage calculation to 500x
  • Separate list of ranked SO terms for structural variants to ensure that the right SO term gets picked as the most severe for SVs
  • Adds option to use bedpe files with svdb query

Tools

  • Arriba: 2.1.0 -> 2.3.0
  • Chromograph 1.1.4 -> 1.3.0
  • DeepVariant: 1.1.0 -> 1.4.0
  • ExpansionHunter: 4.0.2 -> 5.0.0
  • GATK: 4.2.2.0 -> 4.2.6.1
  • HTSlib: 1.13 -> 1.15.1
  • MultiQC: 1.11 -> 1.12
  • Peddy: 0.4.3 -> 0.4.8
  • Picard: 2.25.0 -> 2.27.2
  • SMNCopyNumberCaller 1.1.1 -> 1.1.2
  • Star Fusion: 1.10.1 -> 1.11.0
  • Stranger: 0.8.0 -> 0.8.1
  • Stringtie: 2.1.3b -> 2.2.1
  • Tiddit: 2.12.1 -> 3.3.2
  • Trimgalore: 0.6.4 -> 0.6.7
  • VEP: 104.3 -> 107.0
  • svdb: 2.4.0 -> 2.7.0
  • vcf2cytosure v0.5.1 -> v0.8

Databases

  • clinvar: 20211010 -> 20220829
  • dbnsfp: 4.1a -> 4.3a (grch38 only)
  • gnomad: r3.1.1 -> r3.1.2 (grch38 only)
  • giab: 3.3.2 -> 4.2.1
  • loqusdb dump: 20210921 -> 20220905
  • nist: v3.3.2 -> v4.2.1
  • vcf2cytosure blacklist: 200520
Assets 2
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