Potentially a very stupid question, but it wouldn't be my first ever :)

So looking at the sample VCF files from this Biostars (```subset_hg19.vcf```), I see a bunch of lines with ```0|0``` in them. 

While I realize this means it has identified that position as matching ```REF | REF``` - why would reference matching regions be in the variants file at all? I thought only variants (positions that DID NOT match the REF in one or both alleles) showed up. 

When I run ```bcftools call``` I DONT get any ```0/0```or ```0|0```. Does one have to specifically set the ```call```to identify the matching references - and why would one?

Thanks!

    19      416254  rs192385198     T       C       100     PASS    AC=0;AF=0.000599042;AN=12;NS=2504;DP=18252;EAS_AF=0;AMR_AF=0.0043;AFR_AF=0;EUR_AF=0;SAS_AF=0;AA=T|||;VT=SNP     GT      0|0     0|0     0|0     0|0     0|0     0|0
    19      416335  rs545360745     G       C       100     PASS    AC=0;AF=0.000199681;AN=12;NS=2504;DP=18554;EAS_AF=0;AMR_AF=0;AFR_AF=0.0008;EUR_AF=0;SAS_AF=0;AA=G|||;VT=SNP     GT      0|0     0|0     0|0     0|0     0|0     0|0
    19      416389  rs564036507     G       C       100     PASS    AC=0;AF=0.000199681;AN=12;NS=2504;DP=17931;EAS_AF=0;AMR_AF=0;AFR_AF=0.0008;EUR_AF=0;SAS_AF=0;AA=G|||;VT=SNP     GT      0|0     0|0     0|0     0|0     0|0     0|0
    19      416406  rs185752424     G       A       100     PASS    AC=0;AF=0.000199681;AN=12;NS=2504;DP=17410;EAS_AF=0.001;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0;AA=G|||;VT=SNP      GT      0|0     0|0     0|0     0|0     0|0     0|0
    19      416449  rs929834        C       T       100     PASS    AC=0;AF=0.0924521;AN=12;NS=2504;DP=16305;EAS_AF=0;AMR_AF=0.0216;AFR_AF=0.3336;EUR_AF=0.002;SAS_AF=0.0051;AA=C|||;VT=SNP GT      0|0     0|0     0|0     0|0     0|0
     0|0


You would have this if you create a subset of a bigger vcf.

Say that your vcf contains 100 individuals, for which one has a 1/0 call. The rest of the samples will have 0/0.

It looks like subset_hg19.vcf is a, hm, *subset*, of such a bigger vcf ;-)