step1, step2, step3, and step4 are run in succession to carry out CNV analysis of single cell whole genome sequencing data. The other scripts are invoked in the process.
The following is a basic outline summarizing the analysis:
step1_prepare_and_submit_jobs.sh
(step1) CNV_pipeline_FASTQorBAM_thru_BIN_COUNTS.py
(step1) windowMaker.py
(step1) dupeStats_MOD.py
(step1) Normalize_read_counts_and_segment.R
(step1) Bad_bin_finder.R
step2_remove_badbins_and_reanalyze.sh
(step2) Remove_bad_bins_Segment_Plot.R
step3_find_BIC_CNV_cutoffs.sh
(step3) BIC_n_CNV_cutoff_finder.R
step4_make_cnv_sawtooth_get_summary.sh
(step4) organize_CNVs_for_bedtools_genomecov.R
(step4) plot_genomecov_beds.R
(step4) compute_final_stats.R
These scripts do require some setup to run, including but not limited to installing software tools and packages and editing the hardcoded filepaths.