Hi! Since you have the vcf file already it is implied you have already performed variant calling. What do then mean by identify variants because .vcf file has variants itself.

However if you have the bam file have you decided which tool and utility to use for variant calling? In case, you're using GATK this link maybe helpful: https://gatkforums.broadinstitute.org/gatk/discussion/5894/variant-calling-with-biological-replicate