Is there an improvement in the use of IndelRealigner on bwa-mem bams?

[tatinhawk]

Hi,

I have a couple of WGS bams that I have mapped with bwa-mem and marked the PCR duplicates with Picard. I was wondering, has somebody tried to use GATK's IndelRealigner on bams generated by bwa-mem?
Also, if you have tried, do you know if the realignment really improved the variant calling significantly ?


Thanks!

[dpryan]

Brad Chapman has a number of blog posts that you might be interested in reading. In some of them, he compares different aligners and SNP/Indel calling pipelines. In a few, he uses bwa-mem, though I don't recall off-hand seeing comparisons of with/without indel realignment.

[tatinhawk]

Thanks dpryan I will have a look!!