Protocol for detecting introgressed archaic variants with SPrime

Ying Zhou; Sharon R Browning

doi:10.1016/j.xpro.2021.100550

Protocol for detecting introgressed archaic variants with SPrime

STAR Protoc. 2021 May 19;2(2):100550. doi: 10.1016/j.xpro.2021.100550. eCollection 2021 Jun 18.

Authors

Ying Zhou¹, Sharon R Browning²

Affiliations

¹ Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
² Department of Biostatistics, University of Washington, Seattle, WA 98115, USA.

Abstract

The SPrime program detects the variants in current-day populations that were introgressed from an archaic source in the past. It is optimized for detecting introgression from Neanderthals and Denisovans in modern humans. We provide a protocol for detecting Neanderthal and Denisovan introgression in 1000 Genomes Project data, specifically focusing on the CHB (Han Chinese in Beijing) population. For complete details on the use and execution of this protocol, please refer to Browning et al. (2018).

Keywords: Bioinformatics; Genetics.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Animals
DNA, Ancient / analysis
Genetic Introgression / genetics*
Genomics / methods*
Hominidae / genetics
Humans
Neanderthals / genetics*

Substances

DNA, Ancient

Grants and funding

R01 HG010869/HG/NHGRI NIH HHS/United States