v4.3.0

New Features

• ClinVar annotation from custom annotation files
• Update vcf-report to v4.1.0

v4.2.0

New Features

• Update vcf-report to v4.0.0

v4.1.0

Features:

• Filter per consequence instead of per record

v4.0.1

Changes:

• Bump vip-decision-tree to v2.2.1

v4.0.0

General

New Features

• Rewrite workflow in Nextflow
• Install script to install resources
• Significant performance improvements on clusters due to parallelization
• Command-line interface overhaul
  • Remove Command-line interfaces for individual modules (use start from main command-line interface)
  • Remove force
  • Replace output vcf.gz path with output directory
  • keep only keeps selected intermediate resources
  • assembly is required
  • Rename command-line arguments
• Filter variants based on inheritance match
• Support .vcf / .bcf / .bcf.gz inputs in addition to .vcf.gz
• #145 Use bgzip -l and -@
• #221 Set default vep buffer_size to 500, make configurable
• Introduce test framework with additional tests

Bug Fixes

• Fix #189 Running vip with singularity images in /apps or a subdir results in a warning
• Fix #184 Bam files are a config property rather than a cmd line param
• Fix #182 hg19.fa.gz is an invalid reference sequence filename
• Fix #171 Default reference sequence path
• Fix #5 Improve error handling

Annotation module

New Features

• Add PolyPhen-2 annotations
• Add SIFT annotations
• Give cDNA, CDS and protein positions as Position/Length instead of Position
• Remove VIBE
• #167 Inheritance non-penetrance list should be configurable
• Update gene inheritance_modes resource from 20210920 to 20211119
• Add gnomAD Number of Homozygotes for alt allele and use in default decision tree

Bug Fixes

• Fix #168 Capice precomputed resource files should be configurable

Inheritance matching module

New Features

• Replace Genmod with vip-inheritance-matcher
• Add incomplete penetrance annotation for genes

Bug Fixes

• vip-inheritance-matcher#11 Error running on compounds with symbolic allele
• #169 Compound is missed if one parent is genotyped for each variant
• #151 Inheritance module genmod crash if proband is not affected
• #122 Inheritance module genmod crash for missing VEP annotations

Classification module

New Features

• Rewrite default decision tree
• Use custom exit nodes in decision tree (e.g. B/LB/VUS/LP/P) and filter on custom classes (e.g. VUS/LP/P)

Report module

New Features

• Mark genes associated with incomplete penetrance as such

Bug fixes

• Fix vip-report-api#67 Error on dropped FORMAT field values
• Fix vip-report-api#69 Nested field parsing fails for escaped comma values
• Fix #171 Decision tree rendering: CATEGORICAL without default or missing
• Upgrade igv.js to v2.10.4

v3.3.1

Bug Fixes

• #203 Singularity creates files in users home dir

Features

• Add annotate_vep_custom_gnomAD_GRCh38 default resource

v3.3.0

New Features

• Allow using custom gnomAD annotation file instead of VEP annotations
• GRCh37: Use total (exomes+genomes) gnomAD allele frequencies
  • Additional population frequencies for non-coding variants
  • More accurate population frequencies for many coding variants

v3.2.0

New Features

• Update vkgl_public_consensus_jun2021.tsv to vkgl_public_consensus_sep2021.tsv
• Use variables in config values (e.g. assembly=GRCh38 reference=/data/${assembly}.fa.gz)
• #195 annotate_vep_plugin_VKGL default value should be based on assembly
• MacOS support

Bug Fixes

• Fix #191 artefact plugin broken
• Fix #197 VKGL annotation fails for same gene with different symbol

v3.1.0

New Features

• Update hpo_20210308.tsv to hpo_20210920.tsv
• Update gene_inheritance_modes_20210309.tsv to gene_inheritance_modes_20210920.tsv

v3.0.1

Bug Fixes

• Fix #191 artefact plugin broken