In GATK4 the indel realignment step will no longer be part of the pipeline. With my great surprise the tool has disappeared. My question, the algorithm is no more there because it doesn't improve the alignment? Do I need to search for a replace or should I just remove it from my pipeline since it is not useful? Any suggestions? Thank you Marco
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written
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fabbri.marco •
3 answers
Basically, the realignment step has been integrated into the GATK variant callers and they can output their own realigned BAMs. However, regardless of how you perform realignment, it is still preferred.
To supplement the other answers, there is another discussion here: https://gatkforums.broadinstitute.org/gatk/discussion/11324/gatk4-realignment
In good news (at least in my opinion), the realignment step may be returning to GATK4 at some point: https://github.com/broadinstitute/gatk/issues/3104
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