My data is a VCF file from exome sequencing variant call. I'm not very familiar with the sequencing process and variant calling process. I noticed that there are some missing genotypes, which is recorded as "./." at the GT field. From googling I learned that they're not homozygous reference genotype ("0/0"), but missing calls due to some sequencing ignorance.

In order to make my data "cleaner", I thought it's better to filter out the loci with missing calls if there're not too many of them. I also checked the corresponding "DP" of the loci with and without missing calls. For example:

chr1:123 GT:DP 0/0:2 1/1:4 ./.
chr1:234 GT:DP 0/0:10 1/1:11 1/1:20
chr1:345 GT:DP 0/1:40 1/1:37 0/0:78
chr1:456 GT:DP 0/1:7 0/0:23 ./.
chr1:567 GT:DP 0/1:34 1/1:39 0/0:58

In the above toy example, there're 3 people and 5 loci. I checked the mean DP of all 5 loci and I found that the mean DP of loci with missing calls (1st and 4th loci) to be significantly lower than the mean DP of loci without missing calls (2nd, 3rd and 5th loci). Is that a coincidence? Or are there any specific reason that the loci with missing calls have lower coverage than the "normal" loci? Thanks!

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    $\begingroup$ Have you looked up in the software that made the vcf what ./. means? I would guess it means 0 coverage in that sample at that locus. $\endgroup$ – swbarnes2 Jun 8 '17 at 22:49
  • $\begingroup$ Not that this isn't a useful question here, but there's a newly-started Bioinformatics SE that might like to have a whack at this: bioinformatics.stackexchange.com $\endgroup$ – Gaurav Jun 9 '17 at 18:30
  • $\begingroup$ @swbarnes2 In the documentation, "./." simply means no call. In literatures, there're several different reasons causing this. This could be due to 0 coverage, and also other reasons, which I'm not so clear about. But let's assume that they're caused by 0 coverage, I still don't know the answer to my question. Do you have any ideas? $\endgroup$ – Yan Jun 13 '17 at 1:32

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