I know Quiver and GATK have been bundled in SMRT pipeline to call variants (the GATK module only finds SNPs though). I'm wondering if there are other tool(s) that can be used for this purpose, especially to find large indels. Thanks.
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I have an unsupported version of BLASR that does better alignment across large gaps. I have used this to simply count indel variants (really mobile element insertion) using PacBio reads. PM me if you want access to this; I've been hesitant to post it online since it is on a branch that is not updated with bug fixes, etc.. The unsupported version uses an affine alignment penalty. Without this, bases tend to "bleed" out into gaps and make it difficult to call exactly where a gap is.
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