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
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
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
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load qctool
qctool -g cohort1.bgen -s cohort1.sample -g cohort2.bgen -s \
cohort2.sample -og joined.gen -os joined.sample