How can I print only 1 column from a BAM file at specific coordinate.

For example:

```
ACGTGACGGACGGGGCCA
   TGACGGACGGGGCCA
       GGACGGGGCCA
         ^
```

For example print the column at coord 'x' will return AAA (see example above)
Maybe something like this?

    /package/samtools/samtools mpileup ./your.bam | cut -f 1,2,5

That will give you a chromosome, base position (1-based) and a string similar to what you're looking for, but is case sensitive (strand) and has some other symbols for mismatches, etc.

Check out: http://samtools.sourceforge.net/pileup.shtml