gtfutils / annotate

Annotates genomic positions based on a GTF model

For a given input tab-delimited text file with a valid reference and position column,
this script will add columns for the gene name and intron/exon/utr/intragenic position
within the gene (if the position maps to a gene).

Column counts start at 1.

Usage: gtfutils annotate {options} filename.gtf{.gz} input.txt

    -ref num        Column with reference (default: 1)
    -pos num        Column with pos (1-based) (default: 2)

    -gene_id        Output gene_id (from GTF file)
    -transcript_id  Output transcript_id (from GTF file)
    -gene_name      Output gene_name (from GTF file)
    -gene_location  Output gene location (exon, intron, etc)

    -noheader       The first line is not a header (default: True)