Error - Skipping Invalid Roi

Question

[sharan.janjuha]

Hi,

I am trying to use the command "genome music bmr calc-covg"

genome music bmr calc-covg --bam-list=/home/duttlab/Documents/pathbamfile --output-dir=/home/duttlab/Documents/musicoutput/ --reference-sequence=/home/duttlab/Documents/GRCh37/humang1kv37.fasta --roi-file /home/duttlab/Documents/cervical/755/BT755ROIfiltersorted_1based.roi

and I'm getting the following error:

"Skipping invalid ROI: chrX    44703299    44704123    DUSP21" (for all enteries)

my --bam-list= command contains the path to the bam files, both normal and tumor (tab delimited as specified)

"T755    /home/duttlab/Documents/cervical/755/B755_fixed_sorted_realn_DupRm_recal.bam    /home/duttlab/Documents/cervical/755/T755_fixed_sorted_realn_DupRm_recal.bam"

the roi file is sorted and looks like

1    68934    70162    OR4F5
1    569269    569485    Unknown
1    6354680    6355176    ACOT7
1    8073164    8074463    ERRFI1
1    10381591    10382051    KIF1B
1    11155633    11156155    EXOSC10
1    12836961    12837859    PRAMEF12
1    12888195    12888841    PRAMEF11
1    12918652    12920660    PRAMEF2
1    13695437    13696255    PRAMEF18

the genome reference file is in .fasta format (build GRCh37)

Can somebody please help? Thanks in advance..

Answer 1

[Pierre Lindenbaum]

IMHO, that's a prefix "chr" problem with the chromosome names. Check that your file contains "X" and not "chrX".

[Chris Miller]

Agreed. You can either include the "chr" prefix or not, but be consistent across all of your files.