check-sort-order command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

check-sort-order: command not found

or when using sudo you get the following error message

sudo: check-sort-order: command not found

Solutions to check-sort-order: command not found

How To Fix check-sort-order: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu check-sort-order is provided by ggd-utils package.

ggd-utils is:

Takes a genome file and (currently) a .vcf.gz or a .bed.gz and checks that:

 * a .tbi is present
 * the VCF has ""##fileformat=VCF" as the first
 line
 * the VCF has a #CHROM header
 * the chromosome are in the order specified by
 the genome file (and present)
 * the positions are sorted
 * the positions are <= the chromosome lengths
 defined in the genome file.

As a result, any new genome going into GGD will have a .genome file that will dictate the sort order and presence or absence of the ‘chr’ prefix for chromosomes

To fix this problem, we can install more using the command below.

sudo apt-get -y install ggd-utils

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install ggd-utils.

sudo apt -y install ggd-utils

Or if you have aptitude installed you can use the following command.

sudo aptitude install ggd-utils

Summary

In this tutorial we learn how to fix check-sort-order command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.