Closed Xuelei-Dai closed 3 years ago
Hi,
If I interpret your question correctly, you are asking why some calls in the output file lack a genotype (./.
). SVIM is currently able to estimate genotypes for deletions, insertions, inversions and interspersed duplications (not for tandem duplications). Additionally, it requires a certain minimum number of reads to estimate the genotype. This minimum number can be configured with the --minimum_depth
option and is 3 in your case. Furthermore, it requires calls to have a certain minimum score (configured with the --minimum_score
option). That means that variants detected by less than 3 reads or with a score lower than 3 will not get a genotype.
Does this answer your question?
Cheers David
Hello, I used the
SVIM
to call the HiFi reads SV, in the result of variants.vcf file, which theGT
was./.
, my command is :and I used the HiFi coverage is 20X. Whether need to set some parameters?
Best wishes~