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

Map reads with alternate contigs



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    Genevieve Brandt (she/her)

    Hi Linda Do, it looks like you have come up with a great solution! I believe it should work. After doing that step, follow along with the directions checking if the BAM was aligned with alt-handling to make sure that your solution worked.

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    Linda Do

    Thank you for your answer!

    I will try it!

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