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

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

1.0

BELL

1.0

GAUTSCHI

1.0

NEGISHI

1.0

SCHOLAR

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 -p wholenode        # Partition 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
module biocontainers phg

# Your phg workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers phg

# Your phg workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers phg

# Your phg workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers phg

# Your phg workflow...

#!/bin/bash
#SBATCH -A queue     # Queue 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
module biocontainers phg

# Your phg workflow...