Is it possible to get a gVCF from VCF file and a BAM file? I know I can get a gVCF from BAM file by using HaplotypeCaller for variant calling but my plan is to use a different tool for variant calling.
I suppose it depends on if and how you want to compute your GQ and PL values to remain consistent with your VCF data. There's also the question of your binning criteria if you want to make it a banded gVCF.
But in general, the way I'd do it would be to use genomecov from bedtools and obtain a depth histogram for your BAM. Using that depth histogram, it would be pretty easy to use the position info in tandem with your VCF file to generate a gVCF with depth information. Again, GQ and PL are subjective, as are your banding criteria, but the depth histogram would give you the necessary position and depth-of-coverage data.