Some variants have ./. genotype with no read depth info in VCF file

Question

[barslmn]

Some variants in vcf file has no read depth information and has ./. as genotype even though I can see reads there in IGV. What may be causing this?

Thanks

[Devon Ryan]

You can see everything in IGV, even for reads with low MAPQ and bases with low Phred scores. Have a look at both of those in IGV or at least post an IGV screenshot of an example position.