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

Dragen-mode HaplotypeCaller - zygosities


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    Those are places of multiallelic sites. Have you tried spliting those multiallelics ? I bet some of them are derived from those repeat sites. 

    Have you checked how those multiallelic sites look like in your bam file?

    Can you post may be a picture of a sample site without sample information? 

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