Hi there,

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.

https://csg.sph.umich.edu/abecasis/Merlin/tour/parametric.html

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.

1. How do I create a map file or a file with uniform markers obtained from the vcf files from each individual?

2. 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.