I am trying to use GATK to call germline SNPs and indels. In the previous version of GATK, there used to be an option of genotyping_mode DISCOVERY or GENOTYPE_GIVEN_ALLELES. The default used to be DISCOVERY even though I was specifying it everytime I run the command. I checked the manuel and it seems that this option is no longer valid with the new version of GATK i.e latest one 18.104.22.168. If that's the case; how can I specify how to determine the alternate alleles to use for genotyping ?
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