gff-sort1

Usage

Overview

gff-sort reads a General Feature Format version 3 (GFF3) file from standard input and prints a sorted equivalent to standard output. It sorts according to the following criteria:

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accession (highest priority), case insensitively

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feature identifier, case insensitively and hierarchically

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strand (positive first)

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start position

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length (longest first)

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feature key (lowest priority):

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gene or pseudogene (first)

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mRNA, primary_transcript, or a recombination site such as C_region

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CDS

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exon or intron

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anything else (last)