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