I am an undergraduate biochemistry student and have recently embarked upon a family genetics research project to investigate the underlying genetics of a hereditary health condition which segregates in my family in an autosomal dominant pattern. The underlying gene(s) responsible for this health condition have not been conclusively identified, although there appear to be quite a few published studies which have identified a number of candidate genes and chromosome regions which may be involved. Several family members who share the phenotype have volunteered to have their DNA genotyped by the 23andMe company. I would like to use the data to identify chromosome regions which are shared by family members who are affected by the condition, and then compare the results with the published literature to see if any of these regions have an established association with the condition. Basically, I would like to do a miniature linkage study. 23andMe has built-in software which can be used to identify the chromosome regions shared by two individuals, but not several individuals.
My question is: Is there any software available, preferentially open-source, which can read the SNP raw data file (.txt format) for the purposes I have in mind? I am aware of Haploview, but this program only accepts certain file-types as inputs. Any other suggestions, resources, or other sources of information which may be of help would be greatly appreciated! (Please note that I am only a humble beginner and have no experience with bioinformatics software).