Additional scripts

refFlat2bed.py

Generate a BED file of the genes or exons in the reference genome given in UCSC refFlat.txt format. (Download the input file from UCSC Genome Bioinformatics).

This script can be used in case the original BED file of targeted intervals is unavailable. Subsequent steps of the pipeline will remove probes that did not receive sufficient coverage, including those exons or genes that were not targeted by the sequencing library. However, CNVkit will give much better results if the true targeted intervals can be provided.

reference2targets.py

Extract target and antitarget BED files from a CNVkit reference file. While the batch command does this step automatically when an existing reference is provided, you may find this standalone script useful to recover the target and antitarget BED files that match the reference if those BED files are missing or you’re not sure which ones are correct.

Alternatively, once you have a stable CNVkit reference for your platform, you can use this script to drop the “bad” bins from your target and antitarget BED files (and subsequently built references) to avoid unnecessarily calculating coverage in those bins during future runs.

cnn_updater.py

Update .cnn, .cnr and .cns files previously generated by earlier versions of CNVkit to add a “depth” column used in CNVkit version 0.8.0 and later. The script reads each input file, calculates absolute-scale depth from the file’s existing “log2” column value in each row, and creates a corresponding output file with a modified name – the input files are not modified in-place.

Running this script is not necesssary for new analyses, but may help ease the transition for analyses that have already begun.