- Generate a BED file of the genes or exons in the reference genome given in UCSC refFlat.txt format. 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, better results are expected from CNVkit if the true targeted intervals can be provided.
- Calculate the sequence-accessible coordinates in chromosomes from the given reference genome, treating long spans of ‘N’ characters as the inaccessible regions.