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
Tuike
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