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

which pipeline I should use for the CNV calling

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    Bhanu Gandham

    Hi ,

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    Andrey Smirnov

    Hi Yizhou Wang,

    If your samples are all normal I would suggest using the Germline CNV (gCNV) workflow.  Four, however, is very few samples to do analysis with. Do you have more normal mice samples (preferably untreated) that were sequenced with the same technology/protocols etc? If yes, you could use those sample to build a gCNV model using COHORT workflow and then analyze your samples individually with the CASE workflow.

    Somatic pipeline could also give some meaningful results but only if you are looking for large events (on order of mega-bases), and again you would ideally need a larger set of normal samples to create a panel of normals.

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