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

ApplyBQSR Follow

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    Can you please explain why you use the `use-original-qualities` flag when running ApplyBQSR in the best practices? Isn't the goal to use the new, recalibrated scores?

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