Lancet exploration notebook series: Part 1 TCGA-PBTA comparison varia…

…tions (#557)

* Add exploration notebook

* Add to CircleCI

* update gitiugnore to include a file for this analysis

* Update notebooks

* Add only the one ref file

* Fix circleCI file path

* Update .circleci/config.yml file path

* Rearrange order of CircleCI tests

* Add better documentation

* Fix date

* Update the notebook and plots with redone data

* fix file reference

* Incorporate some @jashapiro suggestions and add more documentation about recent issues

* Fix plot rendering

* Undo accidental bolding

* Push changes of function

* push refreshed notebook

* change to 0, 12 substr for all samples and refresh notebook

Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>

.circleci/config.yml

@@ -173,7 +173,6 @@ jobs:
          #### Add your analysis here ####
          ################################
 
-
       - run:
           name: TCGA SNV Caller Analysis 
           command: ./scripts/run_in_ci.sh bash analyses/snv-callers/run_caller_consensus_analysis-tcga.sh     
@@ -186,6 +185,10 @@ jobs:
           name: Tumor mutation burden with TCGA
           command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/tmb-compare-tcga/compare-tmb.Rmd', clean = TRUE)"
 
+      - run:
+          name: PBTA vs TCGA explore 
+          command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-tests/explore-tcga-pbta.Rmd', clean = TRUE)"
+
       - run:
           name: Lancet WXS vs WGS test
           command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-tests/lancet-paired-WXS-WGS.Rmd', clean = TRUE)"
@@ -194,6 +197,7 @@ jobs:
           name: Lancet padded vs unpadded test
           command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-tests/lancet-padded-vs-unpadded.Rmd', clean = TRUE)"
 
+
        # This analysis was a side concept question and no longer needs to be run. 
        # - run:
           # name: SNV Caller VAF Cutoff Experiment

analyses/snv-callers/.gitignore

@@ -2,3 +2,4 @@
 results
 ref_files/*
 !ref_files/gencode.v19.basic.exome.hg38liftover.bed
+!ref_files/intersect_cds_gencode_liftover_WXS.bed