Neusomatic

Introduction

NeuSomatic is based on deep convolutional neural networks for accurate somatic mutation detection. With properly trained models, it can robustly perform across sequencing platforms, strategies, and conditions. NeuSomatic summarizes and augments sequence alignments in a novel way and incorporates multi-dimensional features to capture variant signals effectively. It is not only a universal but also accurate somatic mutation detection method.

For more information, please check:

Home page: https://github.com/bioinform/neusomatic

Note

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

Versions

Cluster	Version(s)
ANVIL	0.2.1
BELL	0.2.1
GAUTSCHI	0.2.1
NEGISHI	0.2.1
SCHOLAR	0.2.1

Commands

• call.py

• dataloader.py

• extract_postprocess_targets.py

• filter_candidates.py

• generate_dataset.py

• long_read_indelrealign.py

• merge_post_vcfs.py

• merge_tsvs.py

• network.py

• postprocess.py

• preprocess.py

• resolve_scores.py

• resolve_variants.py

• scan_alignments.py

• split_bed.py

• train.py

• utils.py

Module

You can load the modules by:

module load biocontainers
module load neusomatic

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 neusomatic on our clusters:

Anvil

#!/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=neusomatic
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers neusomatic

# Your neusomatic workflow...

Bell, Gautschi, or Negishi

#!/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=neusomatic
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers neusomatic

# Your neusomatic workflow...

Gautschi-AI

#!/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=neusomatic
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers neusomatic

# Your neusomatic workflow...

Gilbreth

#!/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=neusomatic
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers neusomatic

# Your neusomatic workflow...

Scholar

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=neusomatic
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers neusomatic

# Your neusomatic workflow...