I am using GATK version 3.7 and following best practice pipeline as recommended for cohorts analysis. I have called variants using HaplotypeCaller joint genotyping with default parameters from 70 samples. When I went through individual samples I found that the same deletion reported by GATK HaplotypeCaller as homogzygous (1/1:0,14:14) with DP of 14 is shown as heterozygous (0/1:5,8:13) with DP of 13 in IGV. As shown in the picture, Ref bases are GGGCG.
Kindly give your valuable comment on this, Thanks. 