CASM IT

ascatNgs

Somatic copy number analysis using WGS paired end wholegenome sequencing

BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.

cgpBattenberg

Battenberg algorithm and associated implementation script

dockstore-cgpwgs

Dockstore implementation of CGP core WGS analysis

cgpBigWig

BigWig manpulation tools using libBigWig and htslib

ClusterSV

SV clustering

vafCorrect

Calculates the Variant Allele Fraction of variants in VCF files

telomerecat

Telomerecat: The telomere computational analysis tool

VAGrENT

A toolset for comparing genomic variants to reference genome annotation to identify potential biological consequences

dockstore-cgpmap

Mapping using PCAP

cgpRna

strelka2-manta

Container for strelka2 and manta

battenberg

Battenberg R package for subclonal copynumber estimation

crisprReadCountsPy

A tool to count reads for CRISPR.

docker-sigprofiler

gripss

Container for the GRIPSS filtering tool ( hartwigmedical / hmftools) for filtering GRIDSS resutls

pycroquet

python Crispr Read to Oligo QUantification and Evaluation Tool

pygas

python Guide aligned Sequences

vcf_flag_modifier

Python application to remove specific flags from VCF files

battenberg_reference_generation

Made for internal use, not supported by CASM-IT. Will be published by another group.

c-sar-denarius

Interface overlay for c-sar

crisprReadCounts

Code to do read counts for CRISPR data

dockstore-cgp-chksum

cgp-chksum produces md5sum and sha512sum of a file, and optionally POST results

dockstore-cgp-irap

Dockerised iRAP for Dockstore.

dockstore-cgpbigwig

RETIRED: Dockstore implementation of cgpBigWig utility. See https://github.com/cancerit/cgpBigWig/

dockstore-ppcg-gridss

dockstore tool for running GRIDSS

GATK_Eze

parabam

parabam

sequence_utils

General store for sequence utility scripts such as base context calculators

workflow-seq-import

Dockstore workflows to import sequencing files