Ped file contains: 0, -, multibase SNPs, and reverse order genotypes

Question

[biology1234]

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?

[Floris Brenk]

--- In addition some SNPs contain multiple base pairs e.g GAT.

-> These are insertions or deletions

How much of the 0 genotypes and other genotypes remain if you filter for example on --geno and --maf etc ? They should be all gone then...

plink --file INPUT --maf 0.05 --geno 0.05 --hwe 1e-6 --min 0.1 --make-bed --out OUTPUT