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This repository was archived by the owner on Oct 11, 2025. It is now read-only.
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 ?
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