Error with bam-window

Question

[ivivek_ngs]

Dear All,

I am trying to use the bam-window for the first time to prepare the input files for the copyCat package for CNV calling. I do not see much of a documentation resource for running the bam-window. I tried to run on my tumor bam file and was thrown with an error. I would like to know if anyone has information for a manual or a link where I can go through the errors usually faced and how to proceed with it. I could not make much out from google and hence the question. In any case if anyone is willing to answer here I would just put the command and the error here.

softwares/bam-window/build/bin/bam-window tumor.realigned.recal.bam ( Does it not work with GATK reclibrated and realigned bam files?)

Error

ERROR: failed to get library name for read group tumor

Thanks

Answer 1

[ernfrid]

bam-window should work on GATK recalibrated or realigned BAM files. The error you're seeing indicates that there isn't a library name associated with the "tumor" read group id. Does your BAM's header have a @RG ID:tumor line? Does it have a LB: component indicating the name of the library? It needs to. This is used to distinguish what reads are associated with what libraries and properly feed counts to CopyCat.

[ivivek_ngs]

I would put in a more comprehensive way. My sample is T_S7998.realigned.recal.bam. It So the error shows that failed to get library name for the read group tumor. However when I try to see the bam file with samtools view for the header I see

@RG    ID:T_S7998    PL:Illumina    SM:T_S7998

Definitely my the read group is having the specified ID , however I cannot find and LB component.

[ernfrid]

You need to have the LB component populated for this read group in order for the software to work properly. Have you added that and had it successfully run?

Additionally, I can't quite tell if the program is reporting the precise error ERROR: failed to get library name for read group tumoror if it is actually reporting ERROR: failed to get library name for read group T_S7998 as it should.

[ivivek_ngs]

It is reporting as below

ERROR: failed to get library name for read group T_S7998

as it should

How should I add the LB component?

[ernfrid]

You need to alter the header of your BAM file.

For every @RG line, you need to make sure there is a LB tag populated. Each library name should be unique if the library is distinct (don't just put an arbitrary name on the libraries if they are in fact different).

For your line, I would change to something like:

@RG    ID:T_S7998    LB:T_S7998-lib1    PL:Illumina    SM:T_S7998