the variant is bi-allelic in reference and target population (source population is only annotated)
score
Typo: ^"dervied"
add the following on the vcf file: "The genotypes in the VCF file need to be segregating in the combined target and source population, and not contain non-variable sites across these individuals. If more individuals are included (such as potential source individuals), sites only variable in these should not be included.
add to the last section a description of each flag that can be provided (missing: match/mismatch flags)
quantile
^"quanitles", ^"simualted"
"The target and reference sizes need to match the number of chromosomes in the real data to be analyzed."
"The index numbers of source and target populations are defined by the order of their appearance in the demes file."
(the rest is fine to refer to -h)
"In order to simulate a range of recombination rates, the sstar quantile function needs to be performed in replicates with the recombination rate steps, and the output tables need to be merged."
threshold
^"determing"
When specifying a recombination map, simulations with sstar quantile need to be performed in recombination rate steps.
The option "--k" only plays a role depending on the number of recombination steps in the simulations, if I understood correctly. So, that should be mentioned...
matchrate
^"specifiy"
last sentence is a fragment
So I understood correctly that there is no haplotype differentiation at the moment, right? If using phased data, it is treated the same way as unphased data; and a perfectly matching heterozygous segment would have a matchrate of 50%? Maybe we can discuss modifications for future versions (non-urgent).
tract
maybe mention the --diff flag
may be good to explain: "If two possible source genomes are provided, two separate files will be written, with the segments matching one of these two source genomes."
Some (not urgent) suggestions for the manual
Overview
score
quantile
threshold
matchrate
tract
--diffflag