Phg
Introduction
Practical Haplotype Graph (PHG) is a general, graph-based, computational framework that can be used with a variety of skim sequencing methods to infer high-density genotypes directly from low-coverage sequence.
For more information, please check:
Docker hub: https://hub.docker.com/r/maizegenetics/phg
Home page: https://www.maizegenetics.net/phg
Versions
1.0
Commands
CreateConsensi.sh
CreateHaplotypes.sh
CreateReferenceIntervals.sh
CreateSmallDataSet.sh
CreateValidIntervalsFile.sh
IndexPangenome.sh
LoadAssemblyAnchors.sh
LoadGenomeIntervals.sh
ParallelAssemblyAnchorsLoad.sh
RunLiquibaseUpdates.sh
CreateHaplotypesFromBAM.groovy
CreateHaplotypesFromFastq.groovy
CreateHaplotypesFromGVCF.groovy
Module
You can load the modules by:
module load biocontainers
module load phg
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 phg on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=phg
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers phg