Hi,

I did 2 separate runs of variant calling using GATK HaplotypeCaller tool. In one run I used Sample from China (CH)as reference and sample from Germany(GER) as input file. For chromosome 1, I got a total of 38,290 variants.

In another run, I switched the reference i.e I used GER as reference and CH as input. This time I got for chromosome 1: 1,016,045 total variants.

As I understand, I should get the same number of variants as the number of positions that differ between the same pair of samples should not change. I am little confused with this result and was wondering if anybody has an explanation for this.

Thank you.