Wednesday 12 December 2012

bioinformatics - Displaying nucleotide at a single position from RNA-seq reads in a BAM file

How do I display a single nucleotide position from reads in a BAM file? I have been looking at variation using samtools mpileup, but I want to actually just display the nucleotide at the position I am interested in. This seems like you should be able to do it but I can't figure out how.



To be clear I have a BAM file of a bunch of reads. I'm looking to do something like samtools magic reads.bam chr3:10000 where I get back something like:



T T T T T T T T T T T T T T T T T T T A A A A A A A A A A A A A.


I just want to sanity check the output of bcftools by actually looking at the base calls.

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