I have a simple radseq data: parents and multiples offsprings. I used Stacks to call SNPs and I am looking to estimate recombination rate in different regions of my genome.
I found Joinmap (https://www.kyazma.nl/index.php/JoinMap/) but apparently you need a licence for this.
I would like to know if you have any recommendations for free (and/or open source) software to estimate recombination rate from a .vcf file ?
Thanks for your help.