|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.
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