Population-scale SV merging does not produce 0/0 genotypes

[DomManou]

Hello,

I am performing population-scaled SV detection and genotyping using Manta.

I have performed individual SV detection for 300 individuals and then merged all genotyped diploid SV files of samples together. As an end output I got SV-heterozygous (1/1) and SV-homozygous genotypes (0/1) for my samples but no Reference-homozygous genotypes (0/0).

Although group calling produces 0/0 genotypes, my sample size is perhaps large for joint calling. Looking through past issues (namely #122 ), I considered the option of using Paragraph to merge , however I see on the software's expected output that 0/0 genotypes are also not included.

Is there a way that I can force Manta genotyping/merging to produce the much valuable 0/0 genotypes for my cohort? Do you think it is sensible to assume that a missing genotype (./.) should be regarded as 0/0 ?

Best regards,
Domniki