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Id: 57143
Status: new
Priority: 0/
Queue: Bio-SamTools
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Owner: Nobody in particular
Requestors: bimber [...] wisc.edu
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pileup.zip

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  Sun May 02 09:06:19 2010 bimber [...] wisc.edu - Ticket created
Subject: Deletions in Pileup
I have noticed that when there is a deletion relative to the reference, the pileup method reports 2 SNPs: one deletion and one non-indel SNP. According to the padded alignment, there should only be a single deletion reported. I have not seen this issue for insertions relative to the reference. The attached script and sample bam file use a modified version of the SNP caller example posted on CPAN to show this. It will output padded alignments for one read/reference pair to illustrate this. Other information: Linux (fedora 12) Bio-SamTools-1.16 perl 5.10.0 Let me know if there is other information I can provide to help.
Subject: pileup.zip
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  Sun May 02 09:15:29 2010 bimber [...] wisc.edu - Correspondence added
From: bimber [...] wisc.edu
I just noticed the 'is_del' method. Testing with this seems to allow SNPs where the 'indel' method returns 0 to be skipped if they are deletions. is that why this method exists? is there a reason why these positions of deletion are being reported twice - once as a deletion and once as a non-indel? On Sun May 02 09:06:19 2010, bbimber wrote: Show quoted text
> I have noticed that when there is a deletion relative to the reference, > the pileup method reports 2 SNPs: one deletion and one non-indel SNP. > According to the padded alignment, there should only be a single > deletion reported. I have not seen this issue for insertions relative > to the reference. > > The attached script and sample bam file use a modified version of the > SNP caller example posted on CPAN to show this. It will output padded > alignments for one read/reference pair to illustrate this. > > Other information: > Linux (fedora 12) > Bio-SamTools-1.16 > perl 5.10.0 > > Let me know if there is other information I can provide to help.