NAME

FILTER-OVERLAPS - Classify peaks in a BED file according to features in a GFF

SYNOPSIS

filter-overlaps overlaps-file.tsv output-file.tsv feature [feature ...]

PURPOSE

Filter-overlaps filters the output of peak-classifier(1) for GFF features indicated on the command-line.

DESCRIPTION

Features include all those explicitly named in the GFF as well as introns, which are computed as regions between the given exons, promoter regions upstream of the TSS, and intergenic regions that do not map to known features.

Names of features indicated on the command-line must exactly match those in the GFF file, or one of the generated feature types "intron", "upstream" followed by an upstream boundary (representing promoter regions), or "intergenic", for regions not covered by any explicit or generated features.

Promoter regions present in the peak-classifier output depend on the peak-classifier command-line parameters. By default, they include "upstream1000", "upstream10000", and "upstream100000".

Features are prioritized in the order they are presented on the command-line and only one overlap is reported in the output. For example, if a peak overlaps both an exon and an intron, and the command is as follows:

filter-overlaps overlaps.tsv filter-overlaps.tsv intro exon upstream1000

then only the overlap with the intron will be reported in the output.

BUGS

Please report bugs to the author and send patches in unified diff format. (man diff for more information)

AUTHOR