I am trying to calculate background mutation rate to find some genes of interest. I am using MuSiC2 for the job using the following command
... music bmr calc-bmr \ --bam-list input_dir/bam_list \ --maf-file input_dir/myMAF.tsv \ --output-dir output_dir/ \ --reference-sequence input_dir/all_sequences.fa \ --roi-file input_dir/all_coding_exons.tsv
I have 10 normal-tumor paired samples. So my question is, while calculating the bmr using
calc-bmr command, we have to give an argument called bam-list. So I have to give the list of all the 10 tumor-normal bam files in the bam list? Or do I just take one tumor-normal sample using which the above
--maf-file was generated and calculate the bmr.