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!
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!
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