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

Suitability of GermlineCNVCaller for targeted sequening dataset

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    Genevieve Brandt (she/her)

    Hi Kevin Donnelly,

    It definitely would be worth trying the gCNV method depending on how many targets you have. We haven't done a lot of testing running gCNV on anything more sparse than whole exome sequencing data. But it may still get good results even with a few hundred targets. 

    You would want to turn off the bias factors and potentially the GC correction because it would be too many parameters for too few data points. Then you will also want to test and adjust the priors such as p_alt, p_active, interval_psi_scale, potentially others.

    Hope this helps you figure out the method that will work for your data! If you find any information that might help future users, please post here!

    Best,

    Genevieve

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    Lourdes Rosano

    Hi Kevin Donnelly,

    We are also working with gCNV on sequencing data from a targeted gene panel. We wanted to ask you, since our analyses sound very similar: did you manage to gain any insights about the parameter recommendations for this kind of data? We would very much appreciate any information you have. Thank you in advance!

    Best,
    Lourdes

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