I'm trying to use the GERMLINE software to identify IBD segments. For now, I'm just testing it out on the HapMap Phase II Data (http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2006-07_phaseII/phased/) that they tested it on in their paper. For now I'm just doing chromosome 1 of CEU. However, I'm getting an ambiguous segfault error:
0 SNPs have genetic distance Read Markers Reading Markers Complete Match Markers Matching Markers - 0%Segmentation fault (core dumped)
At first, after Matching Markers the percentage goes all the way up to 100%, pauses and then the segfault error occurs. Has anyone had a similar problem or can offer a possible explanation? I'm completely lost as to what it could be. Thank you!