genome music bmr cal-covg

Question

[qwertyuiop201320142015]

Hello,

There is a question in my mind. I have the MAFv2.3 files and roi file, but I do not know how to generate the bam-list files which include tumour bam and normal bam.

Any help will be appreciate! Thank you.

Answer 1

[Pascal]

Not quite sure, but I think only the tumor bam is required. Format is

ID<TAB>Another ID<TAB>path/to/Tumor.bam

Answer 2

[michael.d.mclellan]

Check out http://gmt.genome.wustl.edu/packages/genome-music/genome-music-bmr-calc-covg.html

--bam-list

Provide a file containing sample names and normal/tumor BAM locations for each. Use the tab- delimited format [sample_name normal_bam tumor_bam] per line. Additional columns like clinical data are allowed, but ignored. The sample_name must be the same as the tumor sample names used in the MAF file (16th column, with the header Tumor_Sample_Barcode).