I read the BP,found should do bqsr first ,then do IndelRealigner,
I do not know what that will affect ,any big effects to bam results appears ?
Have a look at this blog post.
P.S. I think originally, the Best Practice was to do BQSR first, then Indel Realignment. Most recently, (before we started recommending no Indel Realignment), the Best Practice was to run Indel Realignment then BQSR.