I am sorry for late response. You can use -chr to set specific chromosomes for the analysis Lide Han
Peicheng, The problem may come from map file. For IBDLD, it requires the SNPs have been arranged from smallest to largest across chromosome in map file. If the SNPs are not sorted, '-nan' will be obtained. Lide Han
IBDLDv3.38 is the version which obtain the most accurate IBD estimate in comparison with all previous ones.I hope many more users can use it.
If you meet some problems, please let me know. Welcome provide some advice.