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

Unexpected SOR value changes

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    Genevieve Brandt (she/her)

    Hi Luca Marcolungo,

    Unfortunately our support team does not offer support for GATK3 or UnifiedGenotyper any more. We are confident that the GATK4 updates with HaplotypeCaller will help your results.

    For the SOR update when you added two samples, see if you can follow along with this calculation to determine why the changes may have occurred: StrandOddsRatio

    Hope this helps,

    Genevieve

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