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

BQSR and VQSR resource sequences


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    Pamela Bretscher

    Hi jingchun liu,

    This type of error generally comes from contigs having a different naming convention in your reference files (Chr20 vs. 20). Could you take a look at this article about this issue as well as the suggestions in this previous forum post to see if it is helpful in adjusting the naming of your contigs?

    Kind regards,


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