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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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Your best option is to create a tab delimited position list file:

chr3    1000

You can then use the samtools mpileup -l pos.txt option

-l FILE      list of positions (chr pos) or regions (BED)

This file can also be in bed format if you are interested in specific regions

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