I have some ddRADseq data from a diploid organism I'm working on.
I've generated an unphased VCF file using freebayes that I wanted to convert into PED file. I was wondering how does VCF to PED conversion deal with unphased VCF data? Because when I further converted PED to FASTA, each of the sample had two reads, and the two reads for each sample were different. So how does the conversion program distinguish two alleles at a heterozygous site for each read?
Hope my question makes sense. Any answers or comments will be appreciated!