Genome Analysis Toolkit

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

VariantsToTable GT not extracting correctly


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    Pamela Bretscher

    Hi Asha Mehta,

    Can you clarify what you mean by "prints a part of the sequence"? The GATK team doesn't support Manta, so I wouldn't know how the generates the GT field, but I would assume that there is simply a difference in the algorithms that is resulting in a different value being printed for different tools. 

    Kind regards,


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