Originally posted by Len Trigg
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Originally posted by Len Trigg View PostJo,
The 1-50bp note is more about the default RTG mapping settings (you'd have to start adjusting the aligner settings to look for longer indels, at somewhat of a speed penalty). The variant caller will happily process anything you throw at it. The mappings in your original screenshot looked fine (in that there were reads spanning the deletion, plus some hanging into it, which all gets correctly taken into account by the caller during it's local realignment to the indel hypotheses, so I would say do *not* trim the ends of the reads after alignment).
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