Summarizing results
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The regions of interest pipeline results in many subfolders. I wrote a script to bring all of the results together in a single file. The script is workflow/roi/summary-table.py After you complete the regions of interest pipeline, you can
python [summary-table.py] [your-output-file] [study-folder] [roi-file] [hap-or-snp]
[roi-file] is by default roi.tsv from the end of workflow/scan. If you changed this folder, e.g. you gave the regions of interest names, then point to that file.
[hap-or-snp] says either you want the analysis results hap of the haplotype-based estimates for frequency and location, or the analysis results snp of the best-ranked variant and its frequency and location.
The output of the pipeline in workflow/scan is roi.tsv. This could be your final analysis if you only care about a selection scan. The prior comment is about hard sweep modeling as well.