Best approach for realignertargetcreator and indelrealigner
Posted in Ask the GATK team | Last updated on


Comments (3)

Hi,

I am trying to decide between two approaches for performing realignment around indels. I have ~600 samples that have been aligned to a very fragmented draft genome assembly. What is best:
1. take each sample and create a list of targets, followed by realignment on each sample.
2. combine all samples into one large bam file and create a list of targets, followed by realignment on the same large bam file.

Also, would there be any advantages in terms of speed with either approach?

Cheers,

Steve


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