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How to call SNPs in low coverage Data using GATK?
I would like to known what would be the best way to call SNPs from low coverage data (4x) using GATK. I want to call SNPs for maize, and there is a hapmap for this specie. Is it possible to use the hapmap data in the SNP calling? or it just can be used for the variant recalibration and these increase the possibility to call SNPs in low coverage data for those SNPs also present in the hapmap?