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:
> Rscript R/compile_reads.R -m $PATH/TO/master_file.csv -o $PATH/TO/results_folder
> Rscript R/filter_calls.R -m $PATH/TO/master_file.csv -o $PATH/TO/results_folder
> Rscript R/SV_incorporation.R -m $PATH/TO/manifest_file.tsv -o $PATH/TO/results_folder
> Rscript R/CNA_processing.R -m $PATH/TO/manifest_file.tsv -o $PATH/TO/results_folder
> Rscript R/plot_all_events.R -m $PATH/TO/manifest_file.tsv -o $PATH/TO/results_folder
> 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