I would like to perform linkage analysis with whole exome data from 7 families = 36 individuals each with a vcf file.
I have completed the merlin installation and associated tutorial. I want to complete a parametric analysis using a dominant inheritance model.
Merlin was recommended but I am happy to use other software it is more straightforward.
My question involves the construction of the .map file and data file.
How do I create a map file or a file with uniform markers obtained from the vcf files from each individual?
Are markers obtained from a reference genome file and annotated to the vcfs?
If you have done this kind of analysis before a step-by-step process of how you conducted the analysis including any file conversions to plink etc would be greatly appreciated.