I have a vcf file (4GB) with SNPs and Indels filtered from a candidate gene list. The file contains merged and sorted data of 9 members of a family, mainly affected by neurodegenerative diseases(complex non-mendelian inheritance diseases). I have to do genetic linkage analysis with a free software/package.

I wanted to use MapDisto but I was told it does not work well with human data and GeneHunter, but it is not free. Currently, I am trying to learn how to use paramlink on R but I am not sure It is the right software and approach. Also, would you suggest doing parametric or non-parametric linkage analysis?

Thank you in advance for your help.