Variant calling in low-coverage whole genome sequencing of a Native American population sample

January 2014

Chris Bizon, Michael Spiegel, Scott A Chasse, Ian R Gizer, Yun Li, Ewa P Malc, Piotr A Mieczkowski, Josh K Sailsbery, Xiaoshu Wang, Cindy L Ehlers and Kirk C Wilhelmsen

Scientists from the University of North Carolina at Chapel Hill tested Thunder, a linkage disequilibrium-aware variant caller, on a community sample of Native Americans and determined that low-coverage whole genome sequencing is better at finding novel variants and associations than fixed-content genotyping arrays. They used Pippin Prep to select fragments of 300 base pairs for sequencing on the HiSeq 2000.

BMC Genomics 2014, 15:85


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