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

Does gCNV works with VCF.

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    Genevieve Brandt (she/her)

    Hi Gerardo Fabián,

    I am going to move your post into our Community Discussions -> General Discussion topic, as the Germline topic is for reporting bugs and issues with GATK.

    You can read more about our forum guidelines and the topics here: Forum Guidelines.

    Best,

    Genevieve

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    Pamela Bretscher

    Hi Gerardo Fabián,

    Germline CNV calling can be done with exome data. In this tutorial for calling germline CNVs, there are many references to the applications of exome data and how to adjust the analysis accordingly. Have you already tried this tutorial, and if so, what sort of issues are you having with the software?

    Kind regards,

    Pamela

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