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Qctool

Qctool is a command-line utility program for manipulation and quality control of gwas datasets and other genome-wide data.

Qctool is available as a module on Apocrita.

Usage

To run the default installed version of Qctool, simply load the qctool module:

$ module load qctool
$ qctool -help

Welcome to qctool
(version: X.Y.Z, revision: unknown)

(C) 2009-2020 University of Oxford

Usage: qctool <options>

To display the list of available options, execute qctool -help.

Example jobs

Serial jobs

Here is an example job running on 1 core and 1GB of memory to convert between bgen and vcf formats:

#!/bin/bash
#SBATCH -n 1               # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=1G   # Request 1GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

module load qctool

qctool -g example.bgen -og example.vcf

Here is an example job running on 1 core and 1GB of memory to combine data into one larger dataset:

#!/bin/bash
#SBATCH -n 1               # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=1G   # Request 1GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

module load qctool

qctool -g cohort1.bgen -s cohort1.sample -g cohort2.bgen -s \
          cohort2.sample -og joined.gen -os joined.sample

References