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

(How to) Map reads to a reference with alternate contigs like GRCH38 Follow

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    Sonia Zumalave

    Very useful tutorial! However, it would be very useful if you specify how to get the reference alt index. Some of the links on the post are broken! thanks in advance. 

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