Base recalibration & realignment without known sites
Posted in Ask the GATK team | Last updated on 2012-10-19 16:51:54

Comments (20)

Dear GATK team,

Thanks a lot for the new GATK version and GATK forum!

I am trying to use GATK for yeast strains. I do not have files of known sites of SNPs/indels. I understand that the BaseRecalibrator must get such a file. Do you suggest to skip calibration and realignment, or is there another way to go here?

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