deletion '*' has quality score in pileup?

luxmare · 06-08-2010, 06:50 PM

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.

FYI:

I constructed pileup file by using the following command

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

epigen · 06-09-2010, 09:19 AM

The base quality is also a place holder just as the * in the reads column.

I found similar occurrences in my data (created with samtools pileup -vcf), e.g.

chr14 65392038 T A 0 0 0 1 * W

Note that the weird consensus A must result from a floating underflow in the MAQ SNP calling model (http://sourceforge.net/apps/mediawik...?title=SAM_FAQ). Although the FAQ answer says that this only happens in repetitive regions, the reference T is upper case and I just checked again in the UCSC Genome Browser for hg19 that there is no repeat. So I guess the reason is that there is only one read.

Torst · 06-11-2010, 06:34 PM

Quote:

Originally Posted by luxmare

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?

I don't know how samtools handles this particularly, but the IDEA of giving a deletion a "quality score" is good. A quality score is essentially just a logarithm of a "probability of error" or "probability that this is wrong". So you can interpret it as a statistical confidence of the deletion being real.

luxmare · 06-13-2010, 04:20 PM

Hi Torst,
Thank you for your reply. I agree with you. Quality scores of deletions is informative. But if the pileup format (made by BWA->SAMtools) was designed based on the IDEA you said, inserted bases should have base quality scores. Actually, however, inserted bases don't have qualities as below. I'm confusing...

chr3 7759 C 4 ..,, SO]^
chr3 7760 C 4 .+1G.,, \\\[ <-- 4 ref-type bases and 1 insertion, but only 4 qualities
chr3 7761 G 4 ..,, GT[a

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06-08-2010, 06:50 PM	#1
luxmare Member Location: Japan Join Date: Feb 2009 Posts: 10	*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. FYI: I constructed pileup file by using the following command $ ./samtools-0.1.7a/samtools pileup -f reference.fa <in.bam> > <out.pileup>

06-09-2010, 09:19 AM	#2
epigen Senior Member Location: Germany Join Date: May 2010 Posts: 101	The base quality is also a place holder just as the * in the reads column. I found similar occurrences in my data (created with samtools pileup -vcf), e.g. chr14 65392038 T A 0 0 0 1 * W Note that the weird consensus A must result from a floating underflow in the MAQ SNP calling model (http://sourceforge.net/apps/mediawik...?title=SAM_FAQ). Although the FAQ answer says that this only happens in repetitive regions, the reference T is upper case and I just checked again in the UCSC Genome Browser for hg19 that there is no repeat. So I guess the reason is that there is only one read.

06-13-2010, 04:20 PM	#4
luxmare Member Location: Japan Join Date: Feb 2009 Posts: 10	Hi Torst, Thank you for your reply. I agree with you. Quality scores of deletions is informative. But if the pileup format (made by BWA->SAMtools) was designed based on the IDEA you said, inserted bases should have base quality scores. Actually, however, inserted bases don't have qualities as below. I'm confusing... chr3 7759 C 4 ..,, SO]^ chr3 7760 C 4 .+1G.,, \\\[ <-- 4 ref-type bases and 1 insertion, but only 4 qualities chr3 7761 G 4 ..,, GT[a