Ascatngs

Introduction

AscatNGS contains the Cancer Genome Projects workflow implementation of the ASCAT copy number algorithm for paired end sequencing.

For more information, please check:
Quay.io: https://quay.io/repository/wtsicgp/ascatngs
Home page: https://github.com/cancerit/ascatNgs

Note

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

Versions

Cluster

Version(s)

ANVIL

4.5.0

BELL

4.5.0

GAUTSCHI

4.5.0

NEGISHI

4.5.0

SCHOLAR

4.5.0

Commands

  • alleleCounter.pl

  • ascatCnToVCF.pl

  • ascatCounts.pl

  • ascatFaiChunk.pl

  • ascatFailedCnCsv.pl

  • ascat.pl

  • ascatSnpPanelFromVcfs.pl

  • ascatSnpPanelGcCorrections.pl

  • ascatSnpPanelGenerator.pl

  • ascatSnpPanelMerge.pl

  • ascatToBigWig.pl

  • bamToBw.pl

  • blast2sam.pl

  • bowtie2sam.pl

  • bwa_aln.pl

  • bwa_mem.pl

  • cgpAppendIdsToVcf.pl

  • cgpVCFSplit.pl

  • export2sam.pl

  • interpolate_sam.pl

  • merge_or_mark.pl

  • novo2sam.pl

  • pkg-config.pl

  • psl2sam.pl

  • sam2vcf.pl

  • samtools.pl

  • seq_cache_populate.pl

  • soap2sam.pl

  • stag-autoschema.pl

  • stag-db.pl

  • stag-diff.pl

  • stag-drawtree.pl

  • stag-filter.pl

  • stag-findsubtree.pl

  • stag-flatten.pl

  • stag-grep.pl

  • stag-handle.pl

  • stag-itext2simple.pl

  • stag-itext2sxpr.pl

  • stag-itext2xml.pl

  • stag-join.pl

  • stag-merge.pl

  • stag-mogrify.pl

  • stag-parse.pl

  • stag-query.pl

  • stag-splitter.pl

  • stag-view.pl

  • stag-xml2itext.pl

  • wgsim_eval.pl

  • xam_coverage_bins.pl

  • zoom2sam.pl

Module

You can load the modules by:

module load biocontainers
module load ascatngs

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

module --force purge
module biocontainers ascatngs

# Your ascatngs 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=ascatngs
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ascatngs

# Your ascatngs 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=ascatngs
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ascatngs

# Your ascatngs 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=ascatngs
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ascatngs

# Your ascatngs workflow...

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

module --force purge
module biocontainers ascatngs

# Your ascatngs workflow...