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DecodeGenetics / graphtyper

Population-scale genotyping using pangenome graphs
http://dx.doi.org/10.1038/ng.3964
MIT License
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vcf_merge for SV #148

Open JoannaTan opened 5 months ago

JoannaTan commented 5 months ago

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 commented 3 months ago

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