Read Depth.

In the data which has this structure

pos      ind1-1     ind1-2     ind2-1    ind2-2
1          20         0         15         100
2          0          1          2          50

There is 20,000 position or call variants because every position means SNP. There are 10 individual every individual has 2 replicates. When I looked at the DP, I found there are many ZEROs. according to many papers they call it gap. because there is no read in this position, what I understand from the data above every replicates has its won read depth.

What can I do with low read depth. maybe it will increase the false positive??