GATK 4.2.0.0 Haplotype caller --genotyping_mode DISCOVERY Option

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M.R-E.H

• April 07, 2021 11:30

Hello;

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 I checked the manuel and it seems that this option is no longer valid with the new version of GATK i.e latest one 4.2.0.0. If that's the case; how can I specify how to determine the alternate alleles to use for genotyping ?

Thanks

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  Genevieve Brandt (she/her)

  • April 07, 2021 15:58

  Hi M.R-E.H,

  I am going to move your post into our Community Discussions -> Documentation Questions topic, as the Germline topic is for reporting bugs and issues with GATK.

  You can read more about our forum guidelines and the topics here: Forum Guidelines.

  Best,

  Genevieve

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  Genevieve Brandt (she/her)

  • April 11, 2021 23:26

  Hi M.R-E.H,

  The discovery mode is still default. If you want the genotype_given_alleles mode, you do not need to specify the genotyping mode, all you need to do is give the set of alleles at which to genotype with the --alleles option.

  Best,

  Genevieve

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