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.
2 answers
GATK removed the IndelRealignment tool when v4 came out as it was a very resource demanding step and HaplotypeCaller was indeed already performing local realignment. If you need to realign your indels before using any other variant calling tool you could always try using previous GATK v3.8 (see archive here), which is the latest major version that implemented that module.
Abra2 link: https://github.com/mozack/abra2 does this quite well for short reads.
We implemented it in our alignment pipeline here as well if interested: https://github.com/MHH-RCUG/Wochenende
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I think ABRA doing this job
Not necessary to so that, see first hit on google for ‚deepvariant realignment indel‘ https://github.com/google/deepvariant/issues/35
Generally, don’t do anything to manipulate data unless a manual clearly instructs you to.