I converted a BED file to PED using PLINK.
However when I look through some of my SNPs I notice that some alleles have "-" and "0" as the called base. I understand "0" is a miscall but what is "-" (searched docs, can't find information).
Sometimes the order of the genotype changes e.g some SNPs contain both:
"AC" and "CA"
"A0" and "0A"
I was under the impression that both of the above are equivalent and therefore the order should be standardized in a PED file?
In addition some SNPs contain multiple base pairs e.g GAT.
Is there something wrong with my PED or BED file?