This repository contains scripts used for the analyses described in the "Collateral mutations induced by translesion DNA synthesis" manuscript.
Short contents:
- isomut_postprocessing.R - template for ancestral-clone based filtering of raw IsoMut hits
- DT40_coverage_filtering.py - extracting mapping qualities and regions of fluctuating coverage for each postfiltered IsoMut hit
- Hayward_et_al_melanoma_Isomut.R - Hard filtering of raw IsoMut hits in the selected melanoma samples from Hayward et al, Nature, 2017
- Hayward_et_al_melanoma_postfilter.py - extracting relevant data for each mutation pair in the melanoma samples to find proper collateral pairs
- denovo_NMF.R - template for de novo NMF