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Hello, I am using beagle 4 to phase several thousand samples (>500 trios) plus some single samples. When using the ibd=true, gt=vcfin.vcf, ped=pedin.ped options without reference samples, the resulting phased genotypes do not match the genotypes in the original VCF.
In about 1/3 of the variants, it assigns the inherited het variant to the wrong parent (the parent that is lacking the variant).
Is there an option to improve the phasing or is this likely an input VCF error?
(i checked the unphased input vcf file and the genotypes appear correct, so the error is likely in the beagle process)
Thanks
In about 1/3 of the variants, it assigns the inherited het variant to the wrong parent (the parent that is lacking the variant).
Is there an option to improve the phasing or is this likely an input VCF error?
(i checked the unphased input vcf file and the genotypes appear correct, so the error is likely in the beagle process)
Thanks