Working with the new 1000 genomes (pilot2) release, there are .bai files associated with the new .bam files. I've used 'samtools pileup' to create the pileup files, but the reference column is populated with 'N'. I am trying to determine the reference base (without simply looking at the ncbi human reference and comparing positions), but can't seem to find out how. Is there a way to a) use the .bai file in the process of making the pileup so the reference base column is filled correctly, or b) extract the reference directly from the .bai file?
Sorry if I've missed something obvious, but I can't find anything in the samtools documentation that answers my question.
Thanks,
Jonathan
Sorry if I've missed something obvious, but I can't find anything in the samtools documentation that answers my question.
Thanks,
Jonathan
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