/
CHANGELOG.Rmd
156 lines (116 loc) · 7.04 KB
/
CHANGELOG.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
---
title: "Changelog"
output: rmarkdown::html_document
---
## v1.0.1
* Date: **2022-11-11**
##### Added
- Logo
## v1.0.0
* Date: **2022-02-25**
* Data updates
* ClinVar
* GWAS catalog
* CIViC
* CancerMine
* KEGG
* Disease Ontology/EFO
* Open Targets Platform,
* UniProt KB
* GENCODE
* Improved detection of secondary variant findings
* CPSR is now implemented as a dedicated R package, depending also on the [pcgrr](https://github.com/sigven/pcgr/tree/master/pcgrr) R package. Running the complete CPSR workflow relies upon installation of [PCGR](https://github.com/sigven/pcgr).
## v0.6.2
* Date: **2021-06-30**
* Data updates: ClinVar, PanelApp, GWAS catalog, CIViC, CancerMine, dbNSFP, KEGG, Disease Ontology/EFO, Open Targets Platform, UniProt KB, GENCODE
* Software upgrades: R v4.1, Bioconductor v3.13, VEP (104) ++
* Improved GWAS track for cancer phenotypes
##### Changed
* TOML-based configuration for CPSR is abandoned, all options to CPSR are now configured through the command-line parameters
##### Added
* Command-line options
* Previously set in TOML file
* `--pop_gnomad`
* `--report_theme`
* `--preserved_info_tags` (previously `custom_tags` (TOML))
* `--custom_list_name`
* `--gwas_p_value`
* `--vcfanno_n_proc` (previously `n_vcfanno_proc (TOML)`)
* `--vep_n_forks` (previously `n_vep_forks (TOML)`)
* `--vep_pick_order`
* `--vep_no_intergenic` (previously `vep_skip_intergenic (TOML)`)
* New options
* `--report_nonfloating_toc` (**NEW**) - add the TOC at the top of the HTML report, not floating at the left of the document
* `--report_table_display` (**NEW**) - choose level of comprehensiveness in interactive data tables (full versus light (default))
* Improved support for noncoding variant interpretation, primarily in the context of variants of uncertain significance (VUS). Annotations will show variants that disrupt/create microRNA target sites (dbMTS), and variants that overlap transcription factor binding sites (critical and non-critical positions). Genomic conservation scores (GERP) are also provided.
* Approx. 100 protein-coding genes have been appended to the [CPSR superpanel (panel 0)](superpanel.html)
##### Fixed
* Code typo ([issue #33](https://github.com/sigven/cpsr/issues/33))
##### Removed
* Command-line Options
* `--conf` - configuration file
## v0.6.1
* Date: **2020-11-30**
##### Added
- Increased number of genes in panel 0: All genes in 42 virtual panels related to cancer conditions in Genomics England PanelApp now also contributes toward panel 0
- Added option in main script (`--clinvar_ignore_noncancer`) that will exclude any query variants (from HTML report and TSV/JSON output) that have been reported and classified for non-cancer related conditions only (in ClinVar)
- this to exclude variants associated with non-cancer related phenotypes
- For the variant biomarker table, the resolution of the reported biomarker mapping is highlighted with designated background colors for the gene (exact/codon - black vs. exon/gene - orange)
##### Fixed
- Bug in GWAS hits retrieval, [Issue #30](https://github.com/sigven/cpsr/issues/18)
- Custom VCF tags (as specified by user in configuration file) not shown in output TSV files
##### Changed
- Removed DisGeNET annotations from output (associations from Open Targets Platform serve same purpose)
- Renamed report section __Genomic Biomarkers__ to __Variant Biomarkers__
- Option `--incidental_findings` changed back to `--secondary_findings` - recommended term to use according to ACMG
- Removed _MOD (mechanism-of-disease)_ from TSV output file
## v0.6.0rc
* Date: **2020-09-24**
- Data updates: ClinVar, GWAS catalog, GENCODE, CIViC, CancerMine, UniProt KB, dbNSFP, Pfam, KEGG, Open Targets Platform, Genomics England PanelApp
- Software updates: VEP 101
##### Fixed
* Duplicated entries in incidental findings
##### Changed
* All arguments to `cpsr.py` are now non-positional
* Arguments to `cpsr.py` are divided into two groups: _required_ and _optional_
* `secondary_findings` is now coined `incidental_findings`
* Option ___gwas:gwas_hits___ in CPSR configuration file is now optional argument `--gwas_findings` in `cpsr.py`
* Option ___classification:clinvar_cpsr___ in CPSR configuration file is now optional argument `--classify_all` in `cpsr.py`
* Option ___maf_imits:maf_gnomad___ in CPSR configuration file is now optional argument `--maf_upper_threshold` in `cpsr.py`
* Option ___secondary_findings:show_sf___ in CPSR configuration file is now optional argument `--incidental_findings` in `cpsr.py`
* Virtual panels is now displayed through HTML (previously static ggplot plot)
* __Settings__ section of report is now divived into three:
* Sample metadata
* Report configuration
* Virtual panel
* Classifications of genes as tumor suppressors/oncogenes are now based on a combination of CancerMine citation count and presence in Network of Cancer Genes
##### Added
* Missing ACMG criterion for classification of silent and intronic variants outside of splice regions (_ACMG_BP7_)
* Missing ACMG criterion for classification of variants in promoter and untranslated regions (_ACMG_BP3_)
* Possibility to create custom virtual panel - any combination of genes from panel 0 provided as a single-column text file with argument `--custom_list`
* Ensured that non-empty datatables pr. tier (__ClinVar__ and __Non-ClinVar__) are set as the active tab
* Improved documentation of variant classification in the __References__ section
* DOIs available for all references
## v0.5.2
* Date: **2019-11-18**
##### Changed
* Definition of pathogenic range (wrt to variant frequency) takes into account population- and position-specific allele numbers - no longer defined only by allele counts (i.e. *AC*) but by *AC* and *AN*
* Moved virtual panel identifier from positional argument to optional argument (`--panel_id`) in `cpsr.py`
##### Added
* Ability to analyze custom panels, provided through option `--custom_panel`. Needs to be defined as BED file with four columns, i.e. chromosome, start, stop, genesymbol
## v0.5.1
* Date: **2019-10-14**
##### Fixed
* Bug in `cpsr_validate_input.py`, [GitHub Issue](https://github.com/sigven/cpsr/issues/18)
* Bug when there are zero variants with a 'PASS' status in VCF - omitting report generation
## v0.5.0
* Date: **2019-09-23**
##### Fixed
* Bug in implementation of ACMG criteria; genes without a known loss-of-function mechanism were handled inappropriately
* Bug in assignment of heterozygous/homozygous states (input VCF)
* Bug in implementation of ACMG_PS1 - Same amino acid change as previously pathogenic variant
* Improved consequence prioritisation for variants with transcript consequences in multiple, distinct cancer predisposition genes
* Upper MAF threshold (as given by user) only applied for unclassified (i.e. non-ClinVar variants)
* Handling of non-coding variants (synonymous, upstream_variants) in the report, no longer excluded
##### Added
* Section on _genomic biomarkers_; indicating which variants in the query VCF that overlaps with existing germline biomarkers (CIViC)