docs update

README.md

@@ -6,21 +6,21 @@ The CPSR workflow is integrated with the framework that underlies the [Personal
 
 *CPSR* accepts a query file from a single case/patient, containing raw germline variant calls encoded in the [VCF](https://samtools.github.io/hts-specs/VCFv4.2.pdf) format (i.e. SNVs/InDels). A comprehensive set of **virtual cancer predisposition gene panels** harvested from the [Genomics England PanelApp](https://panelapp.genomicsengland.co.uk/) allows the user to flexibly put a restriction on which genes and findings are displayed in the cancer predisposition report.
 
-Snapshots of sections in the cancer predisposition genome report (artificial sample, with more findings than usual) are shown below:
+Snapshots of sections in the [quarto](https://quarto.org)-based cancer predisposition genome report (artificial sample, with more findings than usual) are shown below:
 
 ![CPSR views](pkgdown/assets/img/cpsr_sc.png)
 
 ## News
 
--   *May 2024*: **2.x.x release**
+-   *June 2024*: **2.x.x release**
     -   New HTML report generation and layout with [quarto](https://quarto.org/)
     -   Excel output supported
     -   Updated virtual gene panels (Genomics England PanelApp, Cancer Gene Census)
     -   Reference data updates, most importantly including 
-        - ClinVar - May 2024
-        - CIViC - May 2024
-        - GENCODE - v45
-    -   Software updates - VEP 111
+        - ClinVar - June 2024
+        - CIViC - June 2024
+        - GENCODE - v46
+    -   Software updates - VEP 112
     -   Extensive code clean-up and re-structuring
 
 -   *November 2022*: **1.0.1 release**

pkgdown/index.md

@@ -8,15 +8,15 @@ The *Cancer Predisposition Sequencing Reporter (CPSR)* is a computational workfl
 
 *CPSR* accepts a query file with raw germline variant calls (SNVs/InDels) from a single sample (cancer patient), encoded in the [VCF format ](https://samtools.github.io/hts-specs/VCFv4.2.pdf). CPSR conducts comprehensive gene and variant annotation on the input calls, and generates a dedicated _variant HTML report_, that provides the following main functionality:
 
-1) Flexible **selection of cancer predisposition genes** subject to analysis
+1) Flexible **selection of cancer predisposition genes** subject to analysis and reporting
 2) **Variant classification** (*Pathogenic* to _Benign_) through implementation of ACMG guidelines
 3) **Biomarker matching** of sample variants (prognosis, diagnosis, drug sensitivity/resistance)
 4) Reporting of **secondary/incidental findings** (ACMG recommendations)
 
 
 The workflow is integrated with the framework that underlies [Personal Cancer Genome Reporter - PCGR ](https://github.com/sigven/pcgr). While *PCGR* is intended for reporting and analysis of somatic variants detected in a tumor, *CPSR* is intended for reporting and ranking of germline variants in protein-coding genes that are implicated in cancer predisposition and inherited cancer syndromes.
 
-Snapshots of sections in the cancer predisposition genome report:
+Snapshots of sections in the [quarto](https://quarto.org)-based cancer predisposition genome report ((artificial sample, with more findings than usual):
 
 ![](img/cpsr_sc.png)
 
@@ -29,10 +29,10 @@ Snapshots of sections in the cancer predisposition genome report:
   - Excel output supported
   - Updated virtual gene panels (Genomics England PanelApp, Cancer Gene Census)
   - Reference data updates, most importantly including 
-    - ClinVar - May 2024
-    - CIViC - May 2024
-    - GENCODE - v45
-  - Software updates - VEP 111
+    - ClinVar - June 2024
+    - CIViC - June 2024
+    - GENCODE - v46
+  - Software updates - VEP 112
   - Extensive code clean-up and re-structuring
 
 * *November 2022*: **1.0.1 release**

vignettes/output.Rmd

@@ -127,6 +127,7 @@ sequence (picked by VEP's `--flag_pick_allele` option) |
 | `LOSS_OF_FUNCTION` | Loss-of-function variant |
 | `LOF_FILTER` | Loss-of-function filter |
 | `SPLICE_DONOR_RELEVANT` | Logical indicating if variant is located at a particular location near the splice donor site (`+3A/G`, `+4A` or `+5G`) |
+| `BIOMARKER_MATCH` | Variant matches with germline biomarker evidence in CIViC/CGI. Format: <db_source>\|<db_variant_id>\|<db_evidence_id>:<tumor_site>:<clinical_significance>:<evidence_level>:<evidence_type><germline_somatic>\|<matching_type>. Multiple evidence items are separated by '&'. Example: civic|174|EID445:Colon/Rectum:Sensitivity/Response:D:Predictive:Germline&EID446:Colon/Rectum:Sensitivity/Response:D:Predictive:Germline|by_gene_mut. Matching type can be any of `by_genomic_coord`, `by_hgvsp_principal`, `by_hgvsc_principal`,  `by_hgvsp_nonprincipal`, `by_hgvsc_nonprincipal`, `by_codon_principal`, `by_exon_mut_principal`, `by_gene_mut_lof`, `by_gene_mut` |
 | `REGULATORY_ANNOTATION` | Comma-separated list of all variant annotations of `Feature_type`, `RegulatoryFeature`, and `MotifFeature`. Format (separated by a `|`): `<Consequence>`, `<Feature_type>`, `<Feature>`, `<BIOTYPE>`, `<MOTIF_NAME>`, `<MOTIF_POS>`, `<HIGH_INF_POS>`, `<MOTIF_SCORE_CHANGE>`, `<TRANSCRIPTION_FACTORS>` |
 
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