---
name: "gaeval"
section: "1"
platform: "linux"
package: "aegean"
version: "0.16.0+dfsg-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gaeval"
---

# gaeval(1)

calculate coverage and intergrity scores for gene models based on transcript alignments

## NAME

gaeval - calculate coverage and intergrity scores for gene models based on transcript alignments

## SYNOPSIS

**gaeval** \[*options*\] *alignments.gff3 genes.gff3* \[*moregenes.gff3* ...\]

## DESCRIPTION

Basic options:

- **-h**\|--help

  print this help message and exit

- **-v**\|--version

  print version number and exit

-

  Weights for calculating integrity score (must add up to 1.0):

- **-a**\|--alpha: DOUBLE

  introns confirmed, or % expected CDS length for single-exon genes; default is 0.6

- **-b**\|--beta: DOUBLE

  exon coverage; default is 0.3

- **-g**\|--gamma: DOUBLE

  % expected 5' UTR length; default is 0.05

- **-e**\|--epsilon: DOUBLE

  % expected 3' UTR length; default is 0.05

-

  Expected feature lengths for calculating integrity score:

- **-c**\|--exp-cds: INT

  expected CDS length (in bp); default is 400

- **-5**\|--exp-5putr: INT

  expected 5' UTR length; default is 200

- **-3**\|--exp-3putr: INT

  expected 3' UTR length; default is 100