DecodeGenetics
vcf_merge for SV
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
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
