vcf_merge for SV

[JoannaTan]

Hi @hannespetur,

We ran graphtyper2 using v2.5.1 two years ago to re-genotype SVs.
We noticed that vcf_merge in v2.5.1 does not include the --sv parameter.
Can we still merge the SVs across samples using vcf_merge?
Can we also know how vcf_merge compute the QD across samples because i noticed that the QD seems to change when we merge VCF across samples.

Hope to hear from you soon.

Thank you.

Best regards,
Joanna

[hannespetur]

Hey,

I mainly use the vcf_merge subcommand for the SV genotyping, so it should be working in v2.5.1. Sorry, I can't remember why or when the --sv parameter was added.

Quality by depth (QD) and other VCF infos that are directly generated from the present sample calls are all recalculated after the merge.

Best,
Hannes