The interpretation of SV output file

Question

[nina]

I am working on structural variant calling. However, the output file include SVs which have genotype(0/0) with consensus sequence. I know "0/1" means heterozygous mutations and "1/1" means homozygous mutations. Also I know "0/0" means missing alleles. I have thought missing alleles means that it could not detect specific location of the SV event. Does anyone can explain why structural variants that are called with specific sequence have "0/0"?

Answer 1

[d-cameron]

For VCF files, 0 indicates the reference allele, whereas . indicates a missing allele. According to the VCF file format specifications 0/0 means an (unphased) diploid reference at the position in question - ie the SV is not present.

That said, genotyping is problematic for SVs as the genotyping assumption of a given ploidy does not necessarily hold true. There's no guidance in the VCF specification about what tools are supposed to do in such cases so it's up to the tool developers to make a guess, not just write genotype information.

Does anyone can explain why structural variants that are called with specific sequence have "0/0"?

If you have multiple samples in the same VCF file, 0/0 would indicate that the SV in not present in that sample.