My goal is to do phasing using shapeit2 (I don't have haplotype reference panels) and I have .ped and .map files for some populations in A/C/G/T format. AFAIK the .ped file only contains genotypes, but no reference allele information. Shapeit2 generated 2 files:
shapeit.v2.r644.linux.x86_64 \ -B population_A.unphased \ -O population_A.PHASED \ -T 8
- .haps with inferred haplotypes in 0/1 format (each line is a SNP)
- .sample (each line is an individual)
Now I have to read a .ped from other population (related to the same study), and I want to ensure allele coding consistency to maintain inference accuracy.
Is there a way to configure allele encoding in SHAPEIT2?
How do I find which allele was chosen as reference allele in the SHAPEIT2 output?