I have 1500 bacterial clean and sorted alignment bam file and I want to call variant and produce a multisample vcf file including 1500 sample. Bacteria are haploid. Do I need to set ploidy option to 1 or to the number of samples 1500?
You can set the ploidy to 1 when producing your GVCFs. Then, you don't need to set the ploidy in GenotypeGVCFs, as it can determine the ploidy from the input GVCFs
P.S. Have a look at this article.