NuclearHorizontalTransfer

Code accompanying "Horizontal transfer of nuclear DNA in a transmissible cancer"

Submodules

• somatypus_nf
  • Single nucleotide and small indel variant caller. Based on Somatypus, but Nextflow-ified.
• pb_genotyper
  • PacBio variant genotyper.
• snv_analysis_pipeline
  • Postprocessing of Somatypus output - separates germline and somatic variants, does quality filtering, runs Variant Effect Predictor, builds phylogenetic trees.
• cnpipe
  • An R package containing various helper functions for working with copy number data.
• copynumber_calling_pipeline
  • Custom copy number variant calling pipeline. Requires cnpipe.
• nf_population_genetics
  • Nextflow pipeline for population genetics analysis.
• nf_htrnaseq
  • Nextflow pipeline for RNAseq analysis, with extra updated scripts to incorporate PacBio long read phasing info.
• segmentation
  • R package used to run Piecewise Constant Function segmentation as part of the copy number calling pipeline.

Misc

• VAF_correction.R
  • source this file in R to put the function fast_estimate_tumour_vaf in scope
  • this code implements the section "Purity correction of variant allele fraction" given in the Methods section of the paper
  • this function is available separately through cnpipe