Question: Error - Skipping Invalid Roi
gravatar for sharan.janjuha
7.8 years ago by
sharan.janjuha0 wrote:


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..

music coverage • 1.9k views
ADD COMMENTlink modified 7.8 years ago by Pierre Lindenbaum130k • written 7.8 years ago by sharan.janjuha0
gravatar for Pierre Lindenbaum
7.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum130k wrote:

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

ADD COMMENTlink written 7.8 years ago by Pierre Lindenbaum130k

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

ADD REPLYlink written 7.8 years ago by Chris Miller21k
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