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Old 06-08-2010, 06:50 PM   #1
Location: Japan

Join Date: Feb 2009
Posts: 10
Unhappy deletion '*' has quality score in pileup?

I know that asterisks '*' in read bases column represent deletions as place holders in pileup format. But in my data, deletion '*' seems to has base quality score. why deleted bases have base qualities?

In this example, there are 6 bases and 1 deletion at the site 25, and the number of base qualities is 7. Can I simply ignore the base quality 'a' corresponding to the deleted base?

chr1 24 g 7 ,..,-1t.,, ``a]bb\
chr1 25 t 7 ,..*.,, b[baaa`
chr1 26 t 7 ,..,.,, a_baa]_

Thanks in advance.


I constructed pileup file by using the following command

$ ./samtools-0.1.7a/samtools pileup -f reference.fa <in.bam> > <out.pileup>
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