shapeit5
Link to section 'Introduction' of 'shapeit5' Introduction
SHAPEIT5 is a software package to estimate haplotypes in large genotype datasets (WGS and SNP array).
Home page: https://github.com/odelaneau/shapeit5
Link to section 'Versions' of 'shapeit5' Versions
- 5.1.1
Link to section 'Commands' of 'shapeit5' Commands
-
phase_common
-
ligate
-
phase_rare
-
simulate
-
switch
-
xcftools
Link to section 'Module' of 'shapeit5' Module
You can load the modules by:
module load biocontainers
module load shapeit5
Link to section 'Example job' of 'shapeit5' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run shapeit5 on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=shapeit5
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers shapeit5
phase_common --input wgs/target.unrelated.bcf --filter-maf 0.001 --region 1 --map info/chr1.gmap.gz --output tmp/target.scaffold.bcf --thread 8