Releases: Clinical-Genomics/MIP
Releases · Clinical-Genomics/MIP
11.1.1
11.1.0
- 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
11.0.02
11.0.1
11.0.0
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