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Old 08-11-2019, 01:30 PM   #1
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Default BBTools for analyzing Ion Torrent generated data?

We are performing full length plasmid sequencing using Ion Torrent's GeneStudio S5 prime system and are not detecting large INDELs (~150bp) using Torrent Suite software. We have heard that BBTools work great for detecting INDELs with Illumina platform.
Has anyone used BBTools to analyze fastq files generated from Ion Torrent system? Any suggestions will be appreciated!
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Old 08-29-2019, 02:18 PM   #2
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Torrent variant caller uses "flow order" information to significantly improve accuracy. No 3rd party tool incorporates this kind of special handling for Ion data so best to stick with the native variant caller
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