Missing variants in chrMT Phase3

Question

[nitya]

Hi,

I am trying to analyze the 1000 Genomes Phase 3 Chromosomal MT VCF for the MT-ATP6 region (m.8527-m.9204) for general mitochondrial DNA variance. I noticed that not every base pair position is represented in the VCF and am concerned this may impact the analysis. How can I "recover" or account for these missing variants or simply excluding them from the analysis? Thanks!

[Pierre Lindenbaum]

I noticed that not every base pair position is represented in the VCF

the VCF usually only contains the positions where at least one variant was found.