Missing genotype data in .vcf file

[favwiz]

Hi all,
I'm trying to gather genotype data from .vcf files generated using GATK (as part of Illumina's MiSeq Reporter software), but I'm getting odd results.
I'm looking at one variant site, and for individual sample vcf files, I get data when there is a variant (i.e. not homozygous reference) so that's fine.
I'd like to be able to output the data for the hom ref samples - i.e. depth at the site so I can quickly confirm whether the genotype is real (is it really homozygous reference, or a no call?).
I'm looking at the genome vcf files to get this data and for some sites I get a 0/0 call, but for others there is just a "." and when I look at the samples in IGV, the coverage is almost the same at both sites. So, I'm wondering how I can get the info that I want, and also why I would get a 0/0 genotype with all the associated info (GQ, MQ, DP, DPF etc) for some positions and not for others?
I've had a look through previous threads, but can't find any info on this.
Apologies also for my ignorance, I am a complete bioinformatics novice.

[finswimmer]

Hello favwiz,
can you please post an example where the genotype is "0/0" or "."

fin swimmer

[favwiz]

Hi fin swimmer,
Thanks for taking a look at this. I've uploaded the combined gvcf that I'm looking at but have had to remove a few lines to reduce the file size. Let me know if you need more info.
Thanks.

[finswimmer]

Hi,
i didn't work with gVCF until now. If I see it correct you're trying to merge the gvcf files of your samples with vcf-merge. In my understanding vcf-merge cannot handle gvcf files as it doesn't take care of the blocksize.

So as your gvcf files were produced by gatk, CombineGVCFs should be the right tool for merging.

fin swimmer