I would like to perform a linkage analysis on whole exome sequencing data. I've spent the last few days trying to figure out how do this and found many threads and papers. However, I don't know much about informatics and barely understand a word. I know that it might be annoying to explain something that complex to a complete layman but I would be grateful beyond words. I don't have anybody to ask and really need to accomplish this.
My thoughts about the basics: 1. I need files with information about the SNPs in the different family members (I have VCF-files) 2. I need to somehow choose markers out of these SNPs or find a program that does it for me (how are these markers chosen/ what makes a good marker? And what is the format of the output file? ped?) 3. The information about the markers (their location and allele frequencies in general and in the different family members) has to be fused in some kind of file, which must also contain information about the relationship of the family members (How do I get such a file, what is the file format? What is the next step?)
Is that correct? If so, how do I put these steps into actions?
Thanks a lot in advance!