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Old 05-30-2016, 11:18 AM   #1
Autotroph
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Location: Europe

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Default Recombination fraction estimation from VCF file

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.
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