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

Versions

  • 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 -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
ml biocontainers ascatngs