Best approach for realignertargetcreator and indelrealigner

steve1980

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

Geraldine_VdAuwera

Hi Steve,

Actually you don't need to combine the samples in a single BAM file to process them together, you can just pass them all as inputs in a list file.

Realigning them all together is best because then the realignment will be consistent over all of them. That said it can be a lengthy process with a lot of samples, so if you find performance is an issue you can do the target creation on the full list, then realign in batches -- as long as you use the same target intervals file that is completely fine. You can also look into multithreading to speed things up.