Virus polymorphism Segminator

tuija

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Join Date: Apr 2012

Posts: 4
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Virus polymorphism Segminator

09-17-2013, 02:08 AM

I have been using GATK tools (mapping done with Mosaik) and Segminator II (using FASTQ data) to map polymorhism in virus resequencing (Ion Torrent). Comparing the results from these two tools, I did notice that with GATK-Unified Genotyper I did map way less polymorphic sites than using Segminator II. Now I am wondering which would be the best way for variation detection in viruses? Anyone has experience with Segminator II? For a biologist it is a really handy, but would like to have opinions from other users.
Tuike
Tags: polymorphism, segminator, virus
jyoti.sutar92

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Join Date: Oct 2013

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#2

10-23-2013, 11:31 PM

I have exactly similar query for my virus resequencing data. Any help in this regard will be highly appreciated. Please let me know if you manage to get some clue as to which tool will be an ideal one in this scenario.

Jyoti
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