Any standalone tool for INDEL Realignment?

2

Hello,

I am thinking of using DeepVariant to call variants, and in their documentation they didn't mentioned anyhting about INDEL Realignment, so I was thinking of using a tool for indel realignment before calling DeepVariant.

So is there any standalone tool just for INDEL Realignment.

Currently I am using HaplotypeCaller, which by default does the Realignment.

Thank you.


indels


deepvariant


realignment

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