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

Mitochondrial pipeline requirement


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    Hi Sheryl

    I guess the pipeline requires you to calculate median coverage over autosomes using CollectWGSMetrics workflow or any other equivalent tool before you start working on variant calling over MT. 

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