SV in input VCF missed in graphtyper output VCF

[tgong1]

Hi,

I have used manta v1.6.0 for SV discovery and svimmer to create multi-sample VCF as the input for graphtyper v2.7.5 (graphtyper genotype_sv). I found some SVs in my input VCF file missed in the genotype_sv output VCF file. I've checked the missing SVs. All of them are greater than 50 bp. I've also checked the ALT filed of the missing SVs. Some of them have sequences, while some are <DEL>,<INS>,<DUP:TANDEM>. Could you suggest why some SVs are missed? Is there any filtering step that graphtyper have done that I may missed? Any insight or help is appreciated. Let me know if you'd like to have a read on the input and output VCF files.

Thank you, Tingting