Overview of Analysis Workflow

Short descriptions on the steps of analysis

The pipeline aims to generate uniform and useful outputs for analyst in preliminary stage of analysis.

Example command to run through the pipeline:

1. Compile reads

> Rscript R/compile_reads.R -m $PATH/TO/master_file.csv -o $PATH/TO/results_folder

2. Filter calls

> Rscript R/filter_calls.R -m $PATH/TO/master_file.csv -o $PATH/TO/results_folder

3. SV incorporation

> Rscript R/SV_incorporation.R -m $PATH/TO/manifest_file.tsv -o $PATH/TO/results_folder

4. CNA processing

> Rscript R/CNA_processing.R -m $PATH/TO/manifest_file.tsv -o $PATH/TO/results_folder

5. Plot all events

> Rscript R/plot_all_events.R -m $PATH/TO/manifest_file.tsv -o $PATH/TO/results_folder

6. Generate HTML report

> Rscript ~/github/access_data_analysis/reports/create_report.R -md -t ~/github/access_data_analysis/reports/template_days.Rmd -p C-L6H8E2 -r ../results_20Jan2023/results_stringent_hc/C-L6H8E2_SNV_table.csv -tt "Melanoma" -m ../manifest_noDate_days.tsv -o C-L6H8E2_days.html -rc ../results_20Jan2023/CNA_final_call_set -d P-0022907 -ds P-0022907-T01-IM6 -dm /juno/work/ccs/shared/resources/impact/facets/all/P-00229/P-0022907-T01-IM6_P-0022907-N01-IM6/default/P-0022907-T01-IM6_P-0022907-N01-IM6.ccf.maf