breardon/calc_mutational_burden repository overview

⁠calculate_mutational_burden

A lightweight python script to calculate coding mutational burden. https://github.com/brendanreardon/calculate_mutational_burden⁠

⁠Run calculate_mutational_burden

calc_mutburden.py can be run by either editing the wrapper.sh or directly from python. Please edit wrapper.sh or run to include the following details for your given sample

• patient_id: An individual ID for the sample being considered
• snv_handle: Path to a MAF file containing single nucleotide variants
• indel_handle: Path to a MAF file containing insertion or deletion variants
• coverage_handle: Path to text file containing only the number of somatic bases covered

Example:

python calc_mutburden.py -patient_id HCC1143 -snv /path/to/snvs.maf -indel /path/to/indels.maf -coverage /path/to/coverage.txt

Given MAF files should follow the specifications detailed by the NCI⁠. The following variant classifications considered to be coding, and thus are used in the calculation of mutational burden:

• Missense_Mutation
• Nonsense_Mutation
• Splice_Site
• Nonstop_Mutation
• Frame_Shift_Del
• Frame_Shift_Ins
• In_Frame_Del
• In_Frame_Ins