Question: MuSiC2 bmr calculation
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gravatar for banerjeeshayantan
2.5 years ago by
banerjeeshayantan190 wrote:

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.

sequencing music2 • 670 views
ADD COMMENTlink modified 2.5 years ago by Ram32k • written 2.5 years ago by banerjeeshayantan190

The code option, banerjeeshayantan, use it!

ADD REPLYlink written 2.5 years ago by Ram32k
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