CASM IT

CASM IT provide bioinformatic support for Cancer, Ageing and Somatic Mutation group at the Wellcome Sanger Institute

Hinxton, Cambridge, UK

Pinned Repositories

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)
Language:C44 17 458
ascatNgs
Somatic copy number analysis using WGS paired end wholegenome sequencing
Language:Perl70 16 8617
BRASS
Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
Language:Perl57 19 9120
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
Language:C60 18 6813
cgpBattenberg
Battenberg algorithm and associated implementation script
Language:Perl52 25 9116
cgpCaVEManWrapper
Reference implementation of CGP workflow for CaVEMan SNV analysis
Language:Perl6 13 253
cgpPindel
Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
Language:Perl28 16 595
dockstore-cgpwgs
Dockstore implementation of CGP core WGS analysis
Language:Shell30 13 5714
proportionalmultibw
JBrowse plugin to display multiple BigWig tracks as a stacked proportion
Language:JavaScript3 3 101
VAGrENT
A toolset for comparing genomic variants to reference genome annotation to identify potential biological consequences
Language:Perl8 15 297

cancerit/TraFiC
DEPRECATED please see https://gitlab.com/mobilegenomes/TraFiC
Language:Perl1 6 05