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How can I get variants only from homozygous region.
I have DNASeq data of an offspring "C" which is cross of parents "A" and "B". Reference genomes of both "A" and "B" are available. I am interested in getting the variants, which should be in the "A" homozygous region. I am confused which reference to use and how to proceed. Your advice will be very valuable. Thank you.