Hi,
Could you please suggest a good tool or script that is able to calculate recombination fraction (for haploid progeny of diploid parent) starting from a vcf file?
I have the phased genotypes of one diploid individual. I also have the genotypes of "all" the haploid progeny. How would i go about calculating the recombination fraction?
Ideally i would also want to estimate the mutation rate and have someway to control for sequencing error.
Could you please suggest a good tool or script that is able to calculate recombination fraction (for haploid progeny of diploid parent) starting from a vcf file?
I have the phased genotypes of one diploid individual. I also have the genotypes of "all" the haploid progeny. How would i go about calculating the recombination fraction?
Ideally i would also want to estimate the mutation rate and have someway to control for sequencing error.