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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GATK 4.2.0.0 Haplotype caller --genotyping_mode DISCOVERY Option

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    Genevieve Brandt (she/her)

    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)

    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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