Software: AscatNGS
Description
AscatNGS contains the Cancer Genome Projects workflow implementation of the ASCAT copy number algorithm for paired end sequencing.
Available Versions
| Unspecified: | 4.5.0 |
|---|
Quay.io: https://quay.io/repository/wtsicgp/ascatngs
Home page: https://github.com/cancerit/ascatNgs
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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