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

    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!

  • #2
    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.

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    • #3
      Thanks dpryan I will have a look!!

      Comment

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