How to specify pedigree information in multisample calling mode?

fritzsedlazeck / Sniffles

Structural variation caller using third generation sequencing

Other

542 stars 89 forks source link

How to specify pedigree information in multisample calling mode? #420

Open tnguyengel opened 1 year ago

tnguyengel commented 1 year ago

How do we specify pedigree information for families or trios for multisample calling mode?

fritzsedlazeck commented 1 year ago

you cannot right now. Its a gernal merge meaning that it just merges across the samples. The GT field and SUP_VEC field will help you navigate which variants are e.g. de novo in a trio setting or somatic between tissues. Hope that helps Fritz

tnguyengel commented 1 year ago

Do you suggest merging different families or different populations in separate batches so that we can tweak the merge settings to be more aggressive within a family or within a population?