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

somatic CNV PoN


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    Laura Gauthier

    Hi Sheryl,

    These are whole-genome samples? I don't have great intuition here because I've done much more work on the germline side, but I think it's worth trying both approaches: with the Illumina PoN and with the small number of samples on the same technology. Any chance the library prep is "PCR-free"?  If they're not, then I would lean toward the smaller, more similar PoN giving better results because it will better capture sequencing biases that might otherwise appear as copy number events. Using allelic counts in the ModelSegments step will help to improve your results.  High tumor purity (which you probably have no control over at this point) may be required for a project with so few samples.  Your results will also potentially depend on how "active" your cancer type is -- fewer events like thyroid and pancreatic will be harder to find amidst noise the PoN couldn't successfully filter out.

    Best of luck!


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