Pindel zygosity determination

Question

[arya.sagittarius]

Hi, I'm trying to understand how pindel determines zygosity. We ran the same fastq files in two pipelines (one using novoalign and the other using bwa mem). The variant we are looking into gives similar read depth &VAF but with diff zygosity. I was trying to understand why is that so ?

      DP          VAF

Pipeline1 655 0.461058877 Pipeline2 703 0.481374966