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Explore Variant_Classification's Impact on TMB: Part 1: Filter vs no Filter #739

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Sep 2, 2020
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Explore Variant_Classification's Impact on TMB: Part 1: Filter vs no Filter #739

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c261bb2
Add script and Rmd basics
cansavvy Aug 13, 2020
464d4d2
Add no nonsyn filter to steps
cansavvy Aug 14, 2020
d9630f9
Got some basic analyses here.
cansavvy Aug 17, 2020
afaceb5
Edits to script. More polishing.
cansavvy Aug 17, 2020
6a085cc
Add some wording
cansavvy Aug 19, 2020
970bee5
Add the tmb plot comparison; rename
cansavvy Aug 20, 2020
721f1bb
Merge branch 'master' into cansavvy/var_class_investigation
cansavvy Aug 20, 2020
08e7224
Fix render
cansavvy Aug 20, 2020
9702928
Merge remote-tracking branch 'cansavvy/cansavvy/var_class_investigati…
cansavvy Aug 20, 2020
da398de
Fix file path
cansavvy Aug 20, 2020
f9940d1
Add some more notes, re-run
cansavvy Aug 21, 2020
2a29bd3
Merge branch 'master' into cansavvy/var_class_investigation
cansavvy Aug 31, 2020
00f9b26
Get rid of the unnecessary region_size removal step and re-run
cansavvy Sep 1, 2020
0f2225a
Add ratio violin plot
cansavvy Sep 1, 2020
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72 changes: 38 additions & 34 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,19 +15,19 @@ jobs:
- run:
name: List Data Directory Contents
command: ./scripts/run_in_ci.sh ls data/testing

- run:
name: Sample Distribution Analyses
command: ./scripts/run_in_ci.sh bash "analyses/sample-distribution-analysis/run-sample-distribution.sh"

- run:
name: Sample Distribution Figure
command: ./scripts/run_in_ci.sh Rscript figures/scripts/fig1-sample-distribution.R

- run:
name: Transcriptome dimensionality reduction
command: ./scripts/run_in_ci.sh ./analyses/transcriptomic-dimension-reduction/ci-dimension-reduction-plots.sh
command: ./scripts/run_in_ci.sh ./analyses/transcriptomic-dimension-reduction/ci-dimension-reduction-plots.sh

# The analysis no longer needs to be tested as it has been retired and is better covered by 'SNV Caller Analysis' below.
#- run:
# name: Mutect2 vs Strelka2
Expand All @@ -41,17 +41,17 @@ jobs:
command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-HGG/run-molecular-subtyping-HGG.sh

- run:
name: Molecular subtyping - Non-MB/Non-ATRT Embryonal tumors
name: Molecular subtyping - Non-MB/Non-ATRT Embryonal tumors
command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-embryonal/run-embryonal-subtyping.sh

- run:
name: Molecular Subtyping and Plotting - ATRT
command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-ATRT/run-molecular-subtyping-ATRT.sh

- run:
name: Molecular subtyping Chordoma
command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-chordoma/run-molecular-subtyping-chordoma.sh

- run:
name: Molecular subtyping - Ependymoma
command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-EPN/run-molecular-subtyping-EPN.sh
Expand All @@ -62,7 +62,7 @@ jobs:

- run:
name: Molecular Subtyping / Reclassification - EWS
command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-EWS/run_reclassification.sh
command: ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-EWS/run_reclassification.sh

- run:
name: Molecular Subtyping - Compile and incorporate pathology feedback
Expand Down Expand Up @@ -104,28 +104,28 @@ jobs:
name: TP53 NF1 classifier run
command: OPENPBTA_POLYAPLOT=0 ./scripts/run_in_ci.sh bash "analyses/tp53_nf1_score/run_classifier.sh"

# This is deprecated
# This is deprecated
# - run:
# name: ssGSEA Analysis
# command: OPENPBTA_ANOVAPVALUE=0.25 OPENPBTA_TUKEYPVALUE=0.50 OPENPBTA_PERCKEEP=0.50 ./scripts/run_in_ci.sh bash analyses/ssgsea-hallmark/run-ssgsea-hallmark.sh


# The second method - ControlFREEC - was not included as of v6, so the comparison can no longer be performed
# - run:
# name: CNV Caller Comparison
# name: CNV Caller Comparison
# command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/cnv-comparison/01-cnv-comparison-plotting.Rmd', clean = TRUE)"

- run:
name: Independent samples
command: ./scripts/run_in_ci.sh bash analyses/independent-samples/run-independent-samples.sh
command: ./scripts/run_in_ci.sh bash analyses/independent-samples/run-independent-samples.sh

- run:
name: Interaction plot
command: OPENPBTA_ALL=0 ./scripts/run_in_ci.sh bash analyses/interaction-plots/01-create-interaction-plots.sh

- run:
name: Mutational Signatures
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/mutational-signatures/mutational_signatures.Rmd', clean = TRUE)"
name: Mutational Signatures
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/mutational-signatures/mutational_signatures.Rmd', clean = TRUE)"

- run:
name: Chromosomal instability breakpoints
Expand All @@ -138,10 +138,10 @@ jobs:
- run:
name: Focal CN Preparation
command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/focal-cn-file-preparation/run-prepare-cn.sh

- run:
name: Survival analysis
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/survival-analysis/survival-analysis_template.Rmd', params = list(plot_ci = FALSE), clean = TRUE)"
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/survival-analysis/survival-analysis_template.Rmd', params = list(plot_ci = FALSE), clean = TRUE)"

- run:
name: Comparative RNASeq - generate correlation matrix - rsem-tpm.polya
Expand All @@ -162,23 +162,23 @@ jobs:
- run:
name: Oncoprint plotting
command: ./scripts/run_in_ci.sh bash "analyses/oncoprint-landscape/run-oncoprint.sh"

- run:
name: GISTIC Plots
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/cnv-chrom-plot/gistic_plot.Rmd', clean = TRUE)"

- run:
name: CN Status Heatmap
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/cnv-chrom-plot/cn_status_heatmap.Rmd', clean = TRUE)"

- run:
name: Gene set enrichment analysis to generate GSVA scores
command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash "analyses/gene-set-enrichment-analysis/run-gsea.sh"

- run:
name: Fusion Summary
command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash "analyses/fusion-summary/run-new-analysis.sh"

- run:
name: Add Shatterseek
command: ./scripts/run_in_ci.sh Rscript analyses/sv-analysis/02-shatterseek.R
Expand All @@ -190,47 +190,51 @@ jobs:
- run:
name: GISTIC Results Comparison
command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/compare-gistic/run-compare-gistic.sh


################################
#### Add your analysis here ####
################################

- run:
name: RNA-Seq composition
command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/rna-seq-composition/rna-seq-composition.Rmd', clean = TRUE)"

- run:
name: TCGA SNV Caller Analysis
command: ./scripts/run_in_ci.sh bash analyses/snv-callers/run_caller_consensus_analysis-tcga.sh
name: TCGA SNV Caller Analysis
command: ./scripts/run_in_ci.sh bash analyses/snv-callers/run_caller_consensus_analysis-tcga.sh

- run:
name: SNV Caller Analysis
name: SNV Caller Analysis
command: OPENPBTA_VAF_CUTOFF=0.5 ./scripts/run_in_ci.sh bash analyses/snv-callers/run_caller_consensus_analysis-pbta.sh

- run:
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)"

# This analysis was used to explore the TCGA PBTA data when the BED files used to calculate TCGA
- run:
name: Exploration of nonsynonymous filter
command: ./scripts/run_in_ci.sh bash analyses/snv-callers/explore_variant_classifications/run_explorations.sh

# This analysis was used to explore the TCGA PBTA data when the BED files used to calculate TCGA
# were incorrect https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/568
#- run:
# name: PBTA vs TCGA explore
# 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)"

# This analysis arose from 'PBTA vs TCGA explore' and was used to explore Lancet's ability to handle WXS data #- 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)"

# This analysis arose from PBTA vs TCGA explore' and was used to explore Lancet's results with padded vs unpadded
#- run:
# 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.
# This analysis was a side concept question and no longer needs to be run.
# - run:
# name: SNV Caller VAF Cutoff Experiment
# command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/vaf_cutoff_experiment.Rmd', clean = TRUE)"
# command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/vaf_cutoff_experiment.Rmd', clean = TRUE)"

# This checks that the GISTIC install still works, but not the modules code
- run:
Expand All @@ -250,7 +254,7 @@ jobs:
command: ./scripts/run_in_ci.sh bash analyses/survival-analysis/run_survival.sh

deploy:
machine:
machine:
docker_layer_caching: true
working_directory: ~/OpenPBTA-analysis
steps:
Expand Down
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