gtfutils / add_xref

Adds gene name annotations to a GTF file (xref)

This adds gene name annotations based upon the KnownGene annotations from the
UCSC Genome Browser. Gene names will be taken from the kgXref table. This
table must be downloaded separately from the UCSC Genome Browser.

This assumes that the file will be in tab-delimited format and that there is
one line for each transcript. You may specify which column represents the gene
name. In the standard "kgXref.txt" file, this is column #5.

This will add the following attributes:

Usage: gtfutils add_xref {-col num} filename.gtf kgXref.txt

  -col num    The gene name is stored in column {num} (1-based)