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Releases: Clinical-Genomics/MIP

12.1.0

05 Mar 08:51
073b9e5
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What's Changed

  • Adds optional trimming of reads with Fastp for the DNA workflow, turned on by default
  • Adds automatic fail in analaysisrunstatus for cases where the peddy detects errors in the pedigree
  • Adds automatic fail in analaysisrunstatus for cases where the peddy detects a discrepancy between the given and calculated gender

Tools

  • Fastp: 0.23.4

Databases

clinvar: 20231203 -> 20240215
loqusdb snapshot: 20231204 -> 20240220

12.0.3

05 Dec 14:53
9e67ba4
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  • Updates genmod to version 3.8.2 to introduce normalized rankscore, #2055

Tools

  • Genmod 3.7.3 -> 3.8.2

Databases

clinvar: 20230508 -> 20231203
loqusdb snapshot: 20230512 -> 20231204

12.0.2

24 Oct 07:13
443391f
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  • Fixes the relatedness check in MIP, #2057

12.0.1

09 Oct 08:35
ef074ab
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  • fixes #2052
  • adds loqus and gnomad databases to the SV frequency filtering taking place prior to running vcf2cytosure

12.0.0

29 Jun 07:53
31c2fec
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  • 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

11.2.2

09 May 14:06
313d35a
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  • New patch of gens pre processing container to adress issue #2027

Tools

gens_preproc 1.0.8 -> 1.0.11

11.2.1

08 May 10:56
6a63026
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  • Patching of gens pre processing container to solve an issue with incomplete bed files.

Tools

gens_preproc 1.0.2 -> 1.0.8

11.2.0

04 May 07:28
635846d
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Added

  • retroseq workflow for mobile element detection

Databases

  • expansionhunter variant catalog: v4.0.2 -> v5.0.0

11.1.3

27 Mar 14:43
f168961
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  • Adds Gens' bed index file to deliverables

11.1.2

21 Feb 15:43
d68ee90
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Fixed a bug in the mitochondrial deletion recipe affecting samples with 0 intermediate discordant MT reads.