I have 1500 bacterial clean and sorted alignment bam file and I want to call variant and produce a multisample vcf file including 1500 samples. I am going to use GATK and bcftools and then compare results. Bacteria are haploid. In the following commands, -ploidy must be set to 1 or 1500?
bcftools call -m -v --ploidy 1 -O z -o variant.vcf.gz mpileup.bcf
java -jar $GATK -T UnifiedGenotyper -R reference.fa -I bam.list -glm BOTH -stand_call_conf 30 -ploidy 1 -o call.vcf