Simple mutation randomization

Content

Mutation randomization based on trinucleotide context specific mutation rates.

The following topics are covered:

• Trinucleotide context profile
• Mutation rate as normalized trinucleotide context profile
• Randomize mutations based on mutation rate
• Expectation and variance of a score based on mutation rate
• Sample-specific profiles based on prior profiles

Main explainer:

/notebooks/randomization.ipynb

Test data:

/notebooks/create_test_data.ipynb

Environment

conda env create -f environment.yml

bgsignatures: $ pip install bgsignatures

bgreference: conda install -c conda-forge -c bbglab bgreference

Data

The trinucleotide content of the reference exome was downloaded from the SigProfilerMatrixGenerator github:

• triplet count per chromosome in the exome: context_counts_GRCh38_96_exome.csv
• check out other categories: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/tree/master/SigProfilerMatrixGenerator/references/chromosomes/context_distributions