How do I add reference/alternate alleles to my vcf file?

Question

Here are the first few columns of my VCF v4.2 file. As you can see, the alt allele is missing. The VCF's refs and alts don't correspond to the reference genome.

#CHROM	POS	ID	REF	ALT
9	77051	rs9408670	T	C
9	114350	rs12685480	A	.
9	116581	rs558835286	G	.
9	117550	rs267602077	A	.
9	117720	rs10959293	T	.
9	126903	rs62533602	G	A
9	133828	rs78804900	C	T
9	154736	rs200683662	T	.
9	154933	rs17795008	T	G
9	174425	rs2998944	T	C
9	174500	rs142581442	G	.
9	175050	rs62532020	G	A
9	185632	rs2992854	C	A
9	188894	rs3951559	G	A
9	191843	rs3008128	G	A
9	202061	rs117675283	T	.
9	204201	rs10964134	G	A

The missing alt allele happens when the genotype is 0/0. The VCF file isn't saying anything incorrect. However, there is a tool I'm trying to use that filters out "0/."genotypes.

A better way of formatting them (which I'm trying to achieve) would have the ref/alt alleles correspond to the reference genome, and just have a redundant letter in the case of a homozygous genotype.

I'd like my VCF to display the correct alt/ref for that position even if there are no samples with a genotype corresponding to the alt allele. How do I do this? I'm not sure what this process is called.

Ideal output:

#CHROM	POS	ID	REF	ALT
9	77051	rs9408670	T	C
9	114350	rs12685480	A	G
9	116581	rs558835286	G	A

Answer 1

Let me know if you see any potential issues with this solution. It just replaces the dots with random letters (easier/faster than aligning to reference genome).

def add_ref():
    # Directory path
    dir_path = '/path/'

    # Function to process genotypes in each row
    def process_genotypes(row):
        genotypes = np.array([x.split(":")[0] for x in row[9:]])
        if row[4] == "." and not any(val in ["1/1", "0/1", "1/0"] for val in genotypes): # to make sure I'm not introducing an allele that isn't present
            # also can do if row[3] in ["A", "T"]: then random.choice(["C", "G"])
            if row[3] == "A":
                row[4] = "C"
            elif row[3] == "T":
                row[4] = "G"
            elif row[3] == "C":
                row[4] = random.choice(["T"]) # I know
            elif row[3] == "G":
                row[4] = random.choice(["A"])
        return row

    # Get all .vcf.gz files in the directory
    files = glob.glob(dir_path + '*.vcf.gz')

    for file in files:
        print(f"Processing {file}...")
        # Name of the new file
        new_file = os.path.join(dir_path, 'new_' + os.path.basename(file))
        with gzip.open(file, 'rt') as in_f, gzip.open(new_file, 'wt') as out_f:
            for line in in_f:
                if line.startswith('#'):
                    out_f.write(line)
                else:
                    row = line.strip().split('\t')
                    new_row = process_genotypes(row)
                    out_f.write('\t'.join(new_row) + '\n')