hap.py
Link to section 'Introduction' of 'hap.py' Introduction
Hap.py is a tool to compare diploid genotypes at haplotype level.
Docker hub: https://hub.docker.com/r/pkrusche/hap.py
Home page: https://github.com/Illumina/hap.py
Link to section 'Versions' of 'hap.py' Versions
- 0.3.9
Link to section 'Commands' of 'hap.py' Commands
- bamstats.py
- cnx.py
- ftx.py
- guess-ploidy.py
- hap.py
- ovc.py
- plot-roh.py
- pre.py
- qfy.py
- som.py
- varfilter.py
Link to section 'Module' of 'hap.py' Module
You can load the modules by:
module load biocontainers
module load hap.py
Link to section 'Example job' of 'hap.py' 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 hap.py on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hap.py
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers hap.py
hap.py \
example/happy/PG_NA12878_chr21.vcf.gz \
example/happy/NA12878_chr21.vcf.gz \
-f example/happy/PG_Conf_chr21.bed.gz \
-r example/chr21.fa \
-o test