In the Clair 3, they suggest to use SwitchZygosityBasedOnSVCalls script. This script takes a Clair3 VCF and a Sniffle2 VCF as inputs. It switches the zygosity from homozygous to heterozygous of a Clair3 called SNP that matches the following two criteria: 1) AF<=0.7, and 2) the flanking 16bp of the SNP is inside one or more SV deletions given in the Sniffle2 VCF.
In the Clair 3, they suggest to use SwitchZygosityBasedOnSVCalls script. This script takes a Clair3 VCF and a Sniffle2 VCF as inputs. It switches the zygosity from homozygous to heterozygous of a Clair3 called SNP that matches the following two criteria: 1) AF<=0.7, and 2) the flanking 16bp of the SNP is inside one or more SV deletions given in the Sniffle2 VCF.
https://github.com/HKU-BAL/Clair3
It might be interesting to test it and maybe to implement in a following version of this pipeline