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Admixture-aware scan for signatures of local adaptation

SY Stephanie M Yan
RM Rajiv C McCoy

Last updated date: Feb 23, 2022 Views: 684 Forks: 0

original An abbreviated version of this protocol was published in eLife in Sep, 2021
Local adaptation and archaic introgression shape global diversity at human structural variant loci
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Dear Yechao,

 

Thank you very much for your interest in our work. The requested information about the 220 frequency-differentiated SVs can be found in the Zenodo repository associated with the paper at https://doi.org/10.5281/zenodo.4469975. We noticed that the relevant file (selscan_res.txt.gz) we had previously posted was truncated and only included data from a single ancestry component. We have updated the file to include the complete set of results, available for direct download at https://zenodo.org/record/6245629/files/selscan_res.txt.gz?download=1. 

 

The 220 frequency-differentiated SVs can be extracted from this table by selecting all rows for which the percentile ("snp_perc" column) is greater than 0.999. A total of 226 rows meet this criterion, of which 220 SV IDs are unique (as a few SVs are outliers in multiple ancestry components).

 

Thanks again, and please let us know if you have any other questions.

 

Best,

 

Rajiv McCoy and Stephanie Yan

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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Yan, S and McCoy, R(2022). Admixture-aware scan for signatures of local adaptation. Bio-protocol Preprint. bio-protocol.org/prep1543.
  2. Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C. and McCoy, R. C.(2021). Local adaptation and archaic introgression shape global diversity at human structural variant loci. eLife. DOI: 10.7554/eLife.67615

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Biophysics

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