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Releases: Clinical-Genomics/MIP

11.1.1

15 Dec 10:56
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  • Updates chromgraph to version 1.3.1
  • Added vcfanno config version 1.18 to the download config

11.1.0

14 Dec 08:00
67561a6
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  • 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

11.0.3

23 Nov 15:05
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  • No login shell for batch scripts
  • Initiate conda prior to activate of conda env

11.0.02

07 Sep 14:46
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Updates chromograph to version 1.1.5

11.0.1

17 May 13:50
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Patch to fix issues encountered when running DeepVariant.

  • When running Deepvariant, set tmpdir to analysis folder and use intermediate_results_dir.
  • When running DeepVariant via singularity, use the options --no-home and --cleanenv.

11.0.0

12 May 08:07
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Changes and new features

  • HmtNote for annotation of mitochondrial variants in VCF file
  • Mitochondrial deletion analysis
  • GATK Haplotypecaller has been turned off in favour of Deepvariant
  • Introduces possibility to store singularity images locally as a .sif file
  • Increased allele frequency cut off for when a variant is filtered out to 0.7
  • Turned off Star_caller and Telomerecat by default

Tools

  • cyrius v1.1 -> v1.1.1
  • deeptrio 1.1.0-gpu -> 1.2.0-gpu
  • gatk 4.2.0.0 -> 4.2.2.0
  • glnexus v1.3.1 -> v1.4.1
  • HmtNote: 0.7.2
  • htslib: 1.10.2 -> 1.13
  • multiqc 1.10.1 -> v1.11
  • star-fusion 1.10.0 -> 1.10.1
  • vep release_103.1 -> release_104.3

References

  • gnomad: r3.0 -> r3.1.1
  • [NEW] gnomad mt: r3.1
  • clinvar: 20210415 -> 20211010

10.2.5

14 Mar 13:15
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  • Allow slurm quality of service flag to be set to 'express'

10.2.4

10 Mar 12:26
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  • Split Star-Fusion alignment and detection into two recipes
  • Use temp directory with Star-Fusion
  • Resource bump for RNA
  • Limit memory for glnexus
  • Use non-gpu version of Deepvariant by default

10.2.3

28 Jan 13:18
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  • Updates chromograph to version 1.1.4

10.2.2

30 Sep 13:29
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  • Adds median target coverage metric to metrics_deliverable file