Re: [Samtools-help] Characters in pileup read bases field

[Heng Li <lh...@sa...>]

Character "^" marks the start of a read and "$" marks the end. The
character following "^" is the mapping quality of the read (ASCII-33
gives the quality). From such a pileup output it is possible to
reconstruct the entire read, but you cannot do so without these
symbols. You can simple ignore these characters if you do not use
mapping quality. If you use mapping quality and prefer a simpler output,
you may use "pileup -s", although the output becomes larger.

Heng

On Wed, Aug 19, 2009 at 10:16:58AM -0400, Benjamin King wrote:
> Hello,
> 
> Is there a complete description of the possible characters in the read bases field created by samtools pileup?  I believe these are referred to as CIGAR strings.
> 
> There is a lot of useful information in the samtools manual page.  However, I can't decipher some of strings that I've generated including the following.
> 
> 
> 1.       What does the "^F" mean?
> 
> chr9    105019626       T       3       ,^F.^Fa @B7
> 
> chr9    105430949       A       8       ,,,....^F.      CCBBBBCB
> 
> 
> 2.       What does the ":" mean?
> 
> chr9    105001865       C       3       ,,^:.   17B
> 
> 
> 3.       What does the "~" mean?
> 
> chr1       120124682       N       T       39      0       60      4       TtT^~T  >BBA
> 
> 
> 4.       What does the "]" mean?
> 
> chr1       120124507       N       G       33      0       60      2       g^]g    @.
> 
> 
> 5.       What does the "!" mean?
> 
> chr1       120124333       N       A       4       0       0       1       ^!A     B
> 
> 
> 6.       What does the "?" mean?
> 
> chr1       120126381       N       G       33      0       30      2       G^?g    =1
> 
> 
> 7.       What does the "}" mean?
> 
> chr1       120125854       N       A       30      0       60      1       ^}A     A
> 
> 
> Thank you,
> 
> 
> -          Ben
> 

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