Ca I make use of Beagle to identify the shared haplotype among a pair of brothers who are haploid
Hi, I am trying to identify the shared region of genome among several pair of brothers in ant who are haploid. I have run the GATK variant discovery pipeline and currently I have VCF file which have only the Homozygous snps as expected. Now can anyone help me to know whether I can make use of beagle to get the shared/common haplotype information from the pair of brothers.also correct me if I am doing something wrong as I new to this field.
PS as of the VCF is unphased.