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Omission of IndelRealignment in production pipelines using GATK 3.5

It was announced with the release of GATK 3.6 that it is no longer necessary to run IndelRealigner when HaplotypeCaller will be used to call variants.

We are testing the published "prod" single-sample workflow and notice that it is still using GATK 3.5 for the HaplotypeCaller step, but omits IndelRealigner (implicitly, since GATK4 is used for e.g. BQSR and other upstream steps).

Question: Does this mean that the advice not to bother with IndelRealigner prior to running HaplotypeCaller applies to the GATK 3.5 version of HaplotypeCaller as well, not just 3.6 and later?

Best Answer


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