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Is there a consensus minimum number of probes to use as cutoff for GATK CNV pipeline (exome)

JakeCJakeC Member, Broadie

Hello,

I was just wondering if there was a cutoff used for the minimum number of probes that constitutes a segment. For example, there are a few segment calls made up of 2-3 probes that occur at a relatively increased frequency. If it is uncertain whether these calls are artifacts or not, are there additional steps to determine this?

Best,
Jake

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