GCTA¶
GCTA is designed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits and perform other analyses to better understand the genetic architecture of complex traits.
GCTA is available as a module on Apocrita.
Usage¶
To run the default installed version of GCTA, simply load the gcta module:
$ module load gcta
$ gcta64
Usage: gcta64 [options]
For usage documentation, see the basic options published on the GCTA website.
Example jobs¶
Serial jobs¶
Here is an example job running on 1 core and 2GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G
module load gcta
gcta64 --bfile test --make-grm --out test
Here is an example job running on 4 cores and 8GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G
module load gcta
gcta64 --reml --grm test --pheno test.pheno --out test --threads ${NSLOTS}