Hap.py
Introduction
Hap.py is a tool to compare diploid genotypes at haplotype level.
For more information, please check:
Docker hub: https://hub.docker.com/r/pkrusche/hap.py
Home page: https://github.com/Illumina/hap.py
Versions
0.3.9
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
Module
You can load the modules by:
module load biocontainers
module load hap.py
Example job
Warning
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