Utilities for lifting over genome coordinates in C. elegans
Perl Python
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data/CHROMOSOME_DIFFERENCES
liftover
LICENSE
README.md
remap_gff_between_releases.pl
requirements.txt
setup.py
test_coords.txt

README.md

liftover-utils

Utilities for lifting over genome coordinates in C. elegans. Currently supports:

  • BCF/VCF
  • GFF
  • Bed
  • Custom (specify chromosome, start position, and optionally end position)

Makes use of remap_gff_between_releases.pl by Gary Williams.

Usage:
  liftover <file> <release1> <release2> (bcf|vcf|gff|bed)
  liftover <file> <release1> <release2> <chrom_col> <start_pos_column> [<end_pos_column>] [options]

Options:
  -h --help     Show this screen.
  --delim=<delim>  File Delimiter; Default is a tab [default: TAB].

Installation

pip install https://github.com/AndersenLab/liftover-utils/archive/v0.1.tar.gz