Hi,

I am doing some imputation job in Beagle and after phasing and imputation I am getting some individuals having duplicated lines for some SNPs but with SNPs phased differently e.g. an individual with 0/1 for a SNP before phasing ends up with two lines in the vcf file, one with 1|0 and the other 0|1. See a simplified example below for one individual and one SNP.

VCF file before phasing

 #CHROM  POS  snpID        344
1:      9 103 Bovine9       0/1

VCF file after phasing

 #CHROM  POS  snpID        344
1:      9 103 Bovine9       1|0
2:      9 103 Bovine9       0|1

Any help on what could be happening here, is this usual?