[Samtools-help] Running samtools mpileup on BAM that contains colorspace

[Michael G. <mi....@gm...>]

Hi all,
I have some SOLiD data from way back and aligned the reads in colorspace 
to a reference genome via `MosaikAligner`. The output of said assembler 
is a `BAM` file that, if sorted, indexed (both via `samtools`) and 
eventually converted to `SAM`, exhibits information in colorspace.

Now, I would like to call the consensus of the aligned reads via 
`samtools mpileup`, but find that `samtools` cannot map any of the reads.

I presume that this error is the result of colorspace information 
contained within the `BAM` file and that `mpileup` is unsuccessful due 
to this circumstance. How would you proceed here?

*NOTE 1:* Said `BAM` file can be open and viewed without problem via 
`BamView`, which I presume indicates the integrity of the `BAM` file.

Thanks in advance,

Michael Gruenstaeudl
http://blogs.fu-berlin.de/gruenstaeudl/