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Old 03-14-2016, 12:37 AM   #1
tristan dubos
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Default Position of insertion in Homopolymer

Hi all ,

I m using bwa for alignment and Varsan with mpileup to find my variants positions. In this list I found an insertion of A in homopolymer of A and the position of this insertion is the beginning of the homopolymer. I compared this result with an other work (witch analyze data with other bioinformatics tools) with this data set and all of my snp agreed only the insertion of A in homopolymer of A disagreed. In this other work the position of this insertion is the end the homopolymer.
Do you know is there rules for this kind of variant ? Is this difference could come from aligners ?

king regards

Tristan

Last edited by tristan dubos; 03-14-2016 at 06:22 AM.
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Old 03-15-2016, 10:16 AM   #2
m_two
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see https://www.biostars.org/p/66843/
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Old 03-15-2016, 09:14 PM   #3
Brian Bushnell
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Different aligners treat homopolymer indels differently. BBMap always shifts them in the same direction (rightmost, I think). PacBio's BLASR places them seemingly at random within the homopolymer, though it is probably related to the specific quality scores of the bases.
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Old 03-16-2016, 04:56 AM   #4
tristan dubos
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Thank you to you two ! I understand now the number of variants we can miss if we compare it into database (like COSMIC) and don't use the same way too call variants .....
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