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?