Mayo_breast_regional_heterogeneity

Multiregional sampling analysis

00_Data

• We used this pipeline (https://github.com/thw17/Mayo_breast_cancer_heterogeneity_assembly) to assemble and clean our data. We used BAM files output from this pipeline for downstream analyses.

01_somatic_mutation_calling

• Use Varscan to genotype somatic mutations
• Snakefile: MAYO_breastcancer.Snakefile

02_Hla

• HLA typing using HLA-LA (https://github.com/DiltheyLab/HLA-LA)
• Because HLA-LA requires the reads to be mapped to the 1000 Genome version of GRCh38, the first step is to strip the reads from the BAM files using XYalign and map the reads to the 1000 Genome version of GRCh38.
  • Snakefile: strip_rempa.snakefile
  • Config file: strip_remap_config.json
• Run HLA-LA:
  • Snakefile: hla.snakefile
  • Config file: hla_config.json
• After HLA typing, rename the hla directory by running the Python script rename_hla_directory.py

03_neoantigens

generate_peptides:

• Use the program pvacseq to generate peptides (21 mers)
• Snakefile: generate_peptides.snakefile

run_mhcpan

• Use the Python script generate_config.py to generate the config file run_mhcpan_config.json
• Snakefile: run_mhcpan.snakefile

filter_peptides

• Use the Python script generate_hla_list.py to generate a list of hla for each sample
• Use the Bash script filter_peptides.sh for filtering peptides

04_mutational_landscape

1. Plot the number of somatic mutations per sample:

• Use the Rscript plot_num_variants_per_individual.R (under 04_mutational_landscape/tabulate_num_variants)

2. Plot upset plot for all of the somatic mutations

• Scripts are under all_mutations_overlap
• Use the Python script make_database_for_upsetr
• Use the Rscript plot_upset.R

3. Plot upset plot for fixed mutations

• Scripts are under fixed_mutations_overlap
• Use Python script find_fixed_variants.py (Snakefile fixed_variants_analysis.snakefile) to find fixed variants.
• Use Python script make_database_for_upsetr_fixed_variants.py for generating the data for upset plot
• Use the Rscript plot_upset_fixed_mutations.R for plotting.