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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

Pileup output of GATK4 vs. GATK3


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    Genevieve Brandt (she/her)

    Hi Ran Wei,

    We looked through the GATK Pileup code and confirmed that the results should be mostly the same comparing GATK3 and GATK4. There are very small differences with how GATK3 and GATK4 work internally so you might see very minor differences. However, the GATK4 version was built with GATK3 compatibility in mind so you shouldn't have any issues.

    Please let me know if you have any issues or further questions.



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