Describe the bug
Hi!
I tested NEAT read-simulator for the first time, and it works great. However, it produces in the golden.vcf file entries with identical REF and ALT like so:

Chr1  21213   .       A       A       42      PASS    .       GT      1

I don't know if that's voluntary or not, but makes hap.py unhappy (sorry) when I'm trying to compare the golden set with the one produced by my tool.

To Reproduce
Here is the command line I used (I installed the tool through conda)

neat read-simulator -c neat_config.yml -o simulated_data

and the yml file:

reference: genome.fasta
read_len: 150
ploidy: 1
coverage: 15
produce_bam: True
produce_vcf: True
paired_ended: True
fragment_mean: 350
fragment_st_dev: 50
threads: 12
rng_seed: 20260420

Expected behavior
I was hoping for a regular vcf file without identical REF and ALT alleles.

Desktop (please complete the following information):

• OS: AlmaLinux release 8.7
• Browser [e.g. chrome, safari]: I am using the software on an HPC.
• Version: of NEAT? 4.3.6