  Selective sweeps are typically associated with a local reduction of genetic
diversity around the adaptive site. However, selective sweeps can also quickly
carry neutral mutations to observable population frequencies if they arise
early in a sweep and hitchhike with the adaptive allele. We show that the
interplay between mutation and exponential amplification through hitchhiking
results in a characteristic frequency spectrum of the resulting novel haplotype
variation that depends only on the ratio of the mutation rate and the selection
coefficient of the sweep. Based on this result, we develop an estimator for the
selection coefficient driving a sweep. Since this estimator utilizes the novel
variation arising from mutations during a sweep, it does not rely on
preexisting variation and can also be applied to loci that lack recombination.
Compared with standard approaches that infer selection coefficients from the
size of dips in genetic diversity around the adaptive site, our estimator
requires much shorter sequences but sampled at high population depth in order
to capture low-frequency variants; given such data, it consistently outperforms
standard approaches. We investigate analytically and numerically how the
accuracy of our estimator is affected by the decay of the sweep pattern over
time as a consequence of random genetic drift and discuss potential effects of
recombination, soft sweeps, and demography. As an example for its use, we apply
our estimator to deep sequencing data from HIV populations.
