Clinical Genomics MIP Versions Save

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

• 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

• Fixes the relatedness check in MIP, #2057

• fixes #2052
• adds loqus and gnomad databases to the SV frequency filtering taking place prior to running vcf2cytosure

• 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

• New patch of gens pre processing container to adress issue #2027

Tools

gens_preproc 1.0.8 -> 1.0.11

• Patching of gens pre processing container to solve an issue with incomplete bed files.

Tools

gens_preproc 1.0.2 -> 1.0.8

Added

• retroseq workflow for mobile element detection

Databases

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

• Adds Gens' bed index file to deliverables

Fixed a bug in the mitochondrial deletion recipe affecting samples with 0 intermediate discordant MT reads.