gff2gff

name	gff2gff
description	Use when a GFF file needs bcftools/csq-compatible gene and transcript attributes before consequence annotation.
disable-model-invocation	true
user-invocable	true

gff2gff

Quick Start

• Command: zcat in.gff.gz | /home/vimalinx/miniforge3/envs/bio/bin/gff2gff | gzip -c > out.gff.gz
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gff2gff
• Full reference: See references/help.md

When To Use This Tool

• Fix GFF attributes so bcftools csq can recognize genes and transcripts more reliably.
• Add missing ID, biotype, and Name fields when equivalent source attributes such as gene_id, gene_type, gene_name, transcript_id, or transcript_type are present.
• Keep an otherwise-streaming bcftools workflow by reading from stdin and writing normalized GFF to stdout.

Common Patterns

# 1) Normalize a compressed GFF before bcftools/csq
zcat in.gff.gz | \
  /home/vimalinx/miniforge3/envs/bio/bin/gff2gff | \
  gzip -c > out.gff.gz

# 2) Run verbosely to inspect warnings while capturing fixed output
cat input.gff | \
  /home/vimalinx/miniforge3/envs/bio/bin/gff2gff -v \
  > fixed.gff \
  2> gff2gff.log

Recommended Workflow

1. Start from the same GFF you plan to feed into bcftools csq, not from an already manually edited copy.
2. Run gff2gff in a pipe and capture stdout explicitly into a new file.
3. Check stderr for the final "Fixed N records" summary and any warnings about records it could not repair.
4. Test the normalized file with a small bcftools csq run before using it across a whole cohort.

Guardrails

• This is a stdin-to-stdout filter; it does not accept positional input or output filenames.
• -h, -?, and --help work, but --version is treated as an unknown parameter.
• Even successful runs print a repair summary to stderr; capture logs separately from the normalized GFF stream.
• The script is narrowly aimed at bcftools csq compatibility, not broad GFF3 validation or arbitrary format conversion.