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Expected number of variants in WES data
I'm interested to know the approximate number of high quality variants reported in WES data. According to this page on the GATK site - https://software.broadinstitute.org/gatk/documentation/article?id=6308 , this is about 41k. However I observe only about 30 - 32k variants in exome data for CDS regions (Gencode v19). I see similar numbers when I analyzed the 1000 genomes phase 3 calls. I'm not sure why the numbers I get are lower. Any information about the reference for those numbers and what region was used and ranges usually observed would be helpful.