suggestions for manual

[kuhlwilm]

Some (not urgent) suggestions for the manual

Overview

• 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."