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

MarkDuplicates has different duplication metrics than EstimateLibraryComplexity

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    Genevieve Brandt

    Hi Ravi Mandla, we would expect some differences in these metrics because the tools do not work the same. MarkDuplicates uses alignment information to determine duplicates. EstimateLibraryComplexity determines duplicates from the bases of the reads, allowing for some error, ignoring the reference. Hopefully this helps clarify these differences for you!

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