Dear community members,

I have tried several tools and got only unsatisfactory results - maybe you know how to proceed?

I have 3 VCF files from WGS of related patients who are affected by a disease. No variants were found so far which may be responsible, so we try to perform old school linkage analysis. Do you know tools that can make it?

I've tried Beagle + IBD discovery - unsuccesfull, the output blocks do not make any sense. Plink from 1.9 does not supprot the whole family of --hap... flags. MERLIN and other tools from the beginning of the century also are hard to apply and even understand...

A potential size of a control cohort is thousands of high quality VCFs - if it helps for the analysis.