20240621 bundle

sigven · Jun 22, 2024 · 6913fb9 · 6913fb9
1 parent fd88b9d
commit 6913fb9
Show file tree

Hide file tree

Showing 4 changed files with 11 additions and 7 deletions.
diff --git a/pcgr/pcgr_vars.py b/pcgr/pcgr_vars.py
@@ -4,7 +4,7 @@
 
 ## Version - software and bundle
 PCGR_VERSION = __version__
-DB_VERSION = '20240612'
+DB_VERSION = '20240621'
 
 ## Miscellaneous settings
 NCBI_BUILD_MAF = 'GRCh38'

diff --git a/pcgrr/vignettes/annotation_resources.Rmd b/pcgrr/vignettes/annotation_resources.Rmd
@@ -17,7 +17,7 @@ output: rmarkdown::html_document
 
 ### Variant databases of clinical utility
   * [ClinVar](http://www.ncbi.nlm.nih.gov/clinvar/) - database of clinically related variants (June 2024)
-  * [CIViC](http://civic.genome.wustl.edu) - clinical interpretations of variants in cancer (June 6th 2024)
+  * [CIViC](http://civic.genome.wustl.edu) - clinical interpretations of variants in cancer (June 21st 2024)
   * [CGI](http://www.cancergenomeinterpreter.org/biomarkers) - Cancer Genome Interpreter Cancer Biomarkers Database (CGI) (October 18th 2022)
 
 ### Protein domains/functional features
@@ -26,7 +26,7 @@ output: rmarkdown::html_document
 
 ### Knowledge resources on gene and protein targets
   * [CancerMine](https://zenodo.org/record/4925789#.YNT8K5MzY7Q) - Literature-mined database of tumor suppressor genes/proto-oncogenes (v50, March 2023)
-  * [Open Targets Platform](https://www.targetvalidation.org/) - Database on disease-target associations, molecularly targeted drugs and tractability aggregated from multiple sources (literature, pathways, mutations) (2024.03)
+  * [Open Targets Platform](https://www.targetvalidation.org/) - Database on disease-target associations, molecularly targeted drugs and tractability aggregated from multiple sources (literature, pathways, mutations) (2024.06)
 
 ### Notes on variant annotation datasets
 

diff --git a/pcgrr/vignettes/installation.Rmd b/pcgrr/vignettes/installation.Rmd
@@ -16,7 +16,7 @@ require(glue, include.only = "glue")
 ```{r vars, echo=FALSE}
 Sys.setenv(VEP_VERSION = "112")
 Sys.setenv(PCGR_VERSION = "1.4.1.9019")
-Sys.setenv(BUNDLE_VERSION = "20240612")
+Sys.setenv(BUNDLE_VERSION = "20240621")
 VEP_VERSION <- Sys.getenv("VEP_VERSION")
 PCGR_VERSION <- Sys.getenv("PCGR_VERSION")
 BUNDLE_VERSION <- Sys.getenv("BUNDLE_VERSION")
@@ -202,12 +202,14 @@ docker container run -it --rm \
     -v /Users/you/dir1/pcgr_outputs:/mnt/pcgr_outputs \
     sigven/pcgr:${PCGR_VERSION} \
     pcgr \
-      --input_vcf "/mnt/pcgr_inputs/tumor_sampleB.BRCA.vcf.gz" \
+      --input_vcf "/mnt/pcgr_inputs/T001-BRCA.grch38.vcf.gz" \
       --vep_dir "/mnt/.vep" \
       --refdata_dir "/mnt/bundle" \
-      --output_dir "/mnt/pcgr_output_sampleB" \
+      --output_dir "/mnt/pcgr_outputs" \
       --genome_assembly "grch38" \
       --sample_id "SAMPLE_B" \
+      --tumor_dp_tag "TDP" \
+      --tumor_af_tag "TAF" \
       --assay "WGS" \
       --vcf2maf
 ```
@@ -249,5 +251,7 @@ apptainer exec \
     --genome_assembly "grch38" \
     --sample_id "SAMPLE_B" \
     --assay "WGS" \
+    --tumor_dp_tag "TDP" \
+    --tumor_af_tag "TAF" \
     --vcf2maf
 ```
diff --git a/pcgrr/vignettes/running.Rmd b/pcgrr/vignettes/running.Rmd
@@ -307,7 +307,7 @@ pcgr \
     --assay WES \
     --vcf2maf \
     --estimate_signatures \
-    --estimate_msi_status \
+    --estimate_msi \
     --estimate_tmb \
     --force_overwrite
 ```