I apologize in advance if this is a stupid question. I am not very computer literate so this program has been difficult for me to get running.
I am having issues with my bam-list file for the bmr calc-covg command in Genome MuSiC. From the description, it says that that this should be a tab delimited file containing sample names and normal/tumor BAM locations [samplename normalbam tumor_bam] which (I think) I have created. My file has the format as follows:
85040004 /media/sf_OWC_Mercury_Elite_AL_Pro/Input/85040006.bam /media/sf_OWC_Mercury_Elite_AL_Pro/Input/85040004.bam
However, every time I try to run, I get an error saying that my BAM files cannot be found, as follows:
Normal BAM for 85040004 not found: "/media/sf_OWC_Mercury_Elite_AL_Pro/Input/85040006.bam" Tumor BAM for 85040004 not found: "/media/sf_OWC_Mercury_Elite_AL_Pro/Input/85040004.bam"
I know that this is the location for the file so I am wondering why it says the BAM is not found. Is it an issue with my BAM list file or the BAM file itself?
On a side note, do my MAF, genome reference file and ROI file all have to have the same formatting for the chromosome column? For example, does my MAF need to have "chr" in front of the number if my ROI file and .fa file do?
Again, I apologize in advance if I am doing something stupid to get this error.
Thanks a lot,