I am using VarScan for variant calling and I use the bam files from 1000genome as control for my project. I run the bam file through VarScan using default setting and then annotate the vcf using Annovar. However, when I try to compare the vcf generated from VarScan and the vcf from 1000 genome, there are some variants which VarScan hasn't called. For example, for SNP rs10000057 is called in the 1000 genome vcf files but it didn't get any calls in the VarScan generated vcf files. Has anyone experience the same situation as I do? Can anyone explain why?