Glimpse2 phasing returning sites from ref not in sample file

[drneavin]

Hello,

I'm trying to use Glimpse2 phasing as you previously suggested for low-coverage data phasing. I am providing a vcf with genotype likelihoods (as PL) but I'm finding that the base phasing is outputting all reference locations instead of just the locations available in the sample vcf file provided even though I'm not providing the --impute-reference-only-variants parameter. My understanding was that this should only happen if --impute-reference-only-variants is provided in the command. Please let me know if I've misunderstood the use of that parameter.

Here's the command I'm using:

GLIMPSE2_phase_static \
            --input-gl {input.gl} \
            --reference $REF \
            --output {params.output} \
            --threads 16 \
            --log {params.log}

Please let me know if there is any other information that you need.