helixforge utils filter

Tiered output filtering by confidence/evidence/biotype.

Options

Option	Description
--gff3	Input GFF3. (required)
--out	Output filtered GFF3. (required)
--preset	Filter preset [default: custom]. (choices: high_confidence/publication_ready/custom; default: custom)
--min-confidence	Minimum confidence score.
--min-tier	Minimum tier (inclusive).
--max-tier	Maximum tier (inclusive).
--exclude-biotype	Biotype(s) to exclude, repeatable. (repeatable)

Examples

  helixforge utils filter --gff3 helixforge.gff3 --out tier1.gff3 --max-tier 1

  helixforge utils filter --gff3 helixforge.gff3 --out pub.gff3 \
      --preset publication_ready --exclude-biotype transposable_element