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/ ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
