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

Protocol for detecting introgressed archaic variants with SPrime

Ying Zhou  1 , Sharon R Browning  2
Affiliations

Protocol for detecting introgressed archaic variants with SPrime

Ying Zhou et al. STAR Protoc. .

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.

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Conflict of interest statement

The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
Screenshot showing the contents of the tools folder and sprime.jar’s help message
Figure 2
Figure 2
Contour plot of CHB results showing three sources of archaic admixture The peak in the upper left represents ancestry from a group that is closely related to the Altai Denisovan, the peak in the middle left represents ancestry from a group that is distantly related to the Altai Denisovan, the peak on the lower right represents ancestry from Neanderthals, and the peak in the lower left represents other segments which may be false positive introgression calls or introgression from another source.
Figure 3
Figure 3
Screenshot of an excerpt of SPrime’s output
Figure 4
Figure 4
Screenshot of augmented SPrime file with matching to Neanderthal and Denisovan genomes
See this image and copyright information in PMC

References

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