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

GenotypeGVCF too many genotypes

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    Bhanu Gandham

    Hi Victoria Buswell

    For pooled samples our recommendation is to use Mutect2. Can you try to use Mutect2 instead of HaplotypeCaller for your variant calling and let me know if that works better? 

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