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allelecount

Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)

annotatevcf

Annotate vcf file using user supplied data

archcompare

Compares pair of archives, files and folders using user configured tools

ascatngs

Somatic copy number analysis using WGS paired end wholegenome sequencing

autocsa

LEGACY: AutoCSA (Automatic Comparative Sequence Analysis) is a mutation detection program designed to detect small mutations (1-50 bases) in capillary sequence traces. The software is capable of detecting both homozygous and heterozygous base substitutions, as well as small insertions and deletions, to a high sensitivity.

battenberg

Battenberg R package for subclonal copynumber estimation

battenberg_reference_generation

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

brass

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

brass-wdl

WDL descriptor for BRASS

c-sar

Data will be added ahead of poster/conference

c-sar-denarius

Interface overlay for c-sar

casm-smart-phase

Docker and associated CASM utility scripts for Smart-Phase (https://github.com/paulhager/smart-phase)

caveman

SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib

cgp-convert-counts

tools for converting RNAseq count data

cgp-dockstore

Contains scripts and packer builds for cgp-dockstore and Openstack builds

cgp-methpipe

CGP implementation of Nextflow methylseq

cgp_seq_input_val

Sequence data and manifest validation code.

cgpanalysehub

Tools to automate CGHub repository download and process with CGP analysis pipelines.

cgpbattenberg

Battenberg algorithm and associated implementation script

cgpbigwig

BigWig manpulation tools using libBigWig and htslib

cgpbincounts

Generates bin count files as required by PICNIC-NGS and some other tools

cgpbox

DEPRECATED please see dockstore-cgpwgs

cgpbpipe

local repo of bpipe that handles LSF array jobs

cgpcavemanpostprocessing

Flagging add on to CaVEMan

cgpcavemanwrapper

Reference implementation of CGP workflow for CaVEMan SNV analysis

cgpjbrowsetoolkit

Holds publicly useful scripts and tools for JBrowse users and admins

cgpngsqc

Collection of code for checking NSG sequencing results

cgppindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

cgprna

cgpvcf

Vcf file utilities