Not call some variants in some populations?

Question

[star]

I have three VCF files from three populations where I merged all their SNPs together. For some variants, there are genotypes in all population but not for all regions, so I got 'NA', I like to know what does it mean? means: no variant call for this region in samples with 'NA' or can I consider 'NA' variants as reference genotype?

ID         CHROM    chromStart  chromEnd    REF     alleles  pop1   pop2  pop3

rs10084237  chr2    76517559    76517560    T       C,T,     NA      CC    NA   
rs10084293  chr2    70917811    70917812    C       C,T,     CT      TT    TT   
rs10084353  chr2    61020552    61020553    A       A,G,     AG      NA    GG

[Ram]

How did you merge the variants? The exact method you used is what determines what these NAs mean.

Answer 1

[bari.ballew]

To expand on what RamRS said, if you've merged VCFs and not gVCFs, note that VCFs only report a genomic location if there is a variant in that individual, so you are susceptible to a missing data problem. When a variant is reported in A.vcf, but not in B.vcf, the merged file will record the variant as missing "./." for sample B. Does that mean there was insufficient coverage to make a call, or was there plenty of coverage and simply no variant reads? If you're looking exclusively at very rare variants, then sometimes assuming a homozygous reference genotype for missing calls is appropriate, but it depends on the downstream analysis.