SNP and SV Identification in PGGB

[zhengluo-zz]

Hi,
When running the pggb pipeline (with two genomes), the alignment file generated by wfmash may contain a fragment of the selected reference genome that aligns to multiple regions in the other genome (either on the same chromosome or different chromosomes). In this case, during graph construction and VCF file generation, which region will the SNPs be assigned to? How are SVs identified?

Thank you for your time and assistance. Looking forward to your response!