Order Of Realignment/Markduplicates/Recalibration

Question

[Wen.Huang]

Hi all,

I am wondering what is the best order to do alignment processing. GATK best practice v4 (http://www.broadinstitute.org/gatk/guide/topic?name=methods-and-workflows) have different sequences when doing single-lane or multi-sample processing. I don't think the order of recal and dedup matters. However, the order of realn and dedup might matter? What are the considerations to think about and what would be the best practice? I am thinking realn before dedup because the realn step may change alignments for some reads.

Thanks!

Answer 1

[Andreas]

For the sake of completeness here the link to the GATK forum post made by the OP. The answer was: it doesn't matter.

Andreas