Data from: Detecting recent selective sweeps while controlling for mutation rate and background selection

Huber CD, DeGiorgio M, Hellmann I, Nielsen R

Date Published: August 19, 2015

DOI: http://dx.doi.org/10.5061/dryad.23d0f

 

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Title SF2 input files
Downloaded 18 times
Description Frequencies of European human SNPs and fixed differences (x=n) to chimpanzee that was used as input file for SweepFinder2. Original data from: Drmanac R, Sparks AB, Callow MJ et al. (2010) Human genome sequencing using unchained base reads on self-assembling DNA Nanoarrays. Science, 327, 78–81.
Download input_frequencies.zip (129.0 Mb)
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Title Recombination rates
Downloaded 16 times
Description Sex-averaged pedigree-based human recombination rates from deCODE Genetics that was used as input file for SweepFinder2. Original data from: Kong A, Thorleifsson G, Gudbjartsson DF et al. (2010) Fine-scale recombination rate differences between sexes, populations and individuals. Nature, 467, 1099–1103.
Download input_recombination_rates.zip (186.8 Mb)
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Title input_Bvalues
Downloaded 15 times
Description B-value map that was used as input file for SweepFinder2. Original data from: McVicker G, Gordon D, Davis C, Green P (2009) Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet, 5, e1000471. Note that the positions correspond to the positions of the recombination rate and frequency files.
Download input_Bvalues.zip (118.2 Mb)
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Title Human-chimpanzee site frequency spectrum
Downloaded 11 times
Description Whole-genome site frequency spectrum (SFS) that includes the proportion of sites that are fixed to chimpanzee (x=n). This file was used as background SFS for SweepFinder2.
Download humanChimpSpectrum.txt (294 bytes)
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When using this data, please cite the original publication:

Huber CD, DeGiorgio M, Hellmann I, Nielsen R (2016) Detecting recent selective sweeps while controlling for mutation rate and background selection. Molecular Ecology 25(1): 142–156. http://dx.doi.org/10.1111/mec.13351

Additionally, please cite the Dryad data package:

Huber CD, DeGiorgio M, Hellmann I, Nielsen R (2015) Data from: Detecting recent selective sweeps while controlling for mutation rate and background selection. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.23d0f
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