CASM IT's Projects
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)
Annotate vcf file using user supplied data
Compares pair of archives, files and folders using user configured tools
Somatic copy number analysis using WGS paired end wholegenome sequencing
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 R package for subclonal copynumber estimation
Made for internal use, not supported by CASM-IT. Will be published by another group.
Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
WDL descriptor for BRASS
Data will be added ahead of poster/conference
Interface overlay for c-sar
Docker and associated CASM utility scripts for Smart-Phase (https://github.com/paulhager/smart-phase)
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
tools for converting RNAseq count data
Contains scripts and packer builds for cgp-dockstore and Openstack builds
CGP implementation of Nextflow methylseq
Sequence data and manifest validation code.
Tools to automate CGHub repository download and process with CGP analysis pipelines.
Battenberg algorithm and associated implementation script
BigWig manpulation tools using libBigWig and htslib
Generates bin count files as required by PICNIC-NGS and some other tools
DEPRECATED please see dockstore-cgpwgs
local repo of bpipe that handles LSF array jobs
Flagging add on to CaVEMan
Reference implementation of CGP workflow for CaVEMan SNV analysis
Holds publicly useful scripts and tools for JBrowse users and admins
Collection of code for checking NSG sequencing results
Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
Vcf file utilities