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)
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.
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
cgpCaVEManWrapper
Reference implementation of CGP workflow for CaVEMan SNV analysis
cgpPindel
Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
cgpRna
PCAP-core
NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)
vafCorrect
Calculates the Variant Allele Fraction of variants in VCF files
VAGrENT
A toolset for comparing genomic variants to reference genome annotation to identify potential biological consequences
AndyMenzies's Repositories
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