AndyMenzies

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:C4317458

• ascatNgs

  Somatic copy number analysis using WGS paired end wholegenome sequencing

  Language:Perl67178517

• BRASS

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

  Language:Perl57209020

• 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:C60196713

• cgpCaVEManWrapper

  Reference implementation of CGP workflow for CaVEMan SNV analysis

  Language:Perl614253

• cgpPindel

  Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

  Language:Perl2717597

• cgpRna

  Language:Perl513144

• PCAP-core

  NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)

  Language:Perl9123710

• vafCorrect

  Calculates the Variant Allele Fraction of variants in VCF files

  Language:Perl1916363

• VAGrENT

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

  Language:Perl816287

AndyMenzies's Repositories