I'm trying to use BEAGLE4 to do an IBD analysis. My files are in PLINK format, thus I used PLINK (v1.9) to generate the VCF file (with the "--recode vcf" flag). Unfortunately I have duplicated markers in the same position (as pointed out by a Beagle exception).
According to the PLINK documentation I could use the flag "--list-duplicate-vars" to identify and then remove them (with the flag --exclude), but when I run it PLINK with the following command:
$ plink --file myfile --list-duplicate-vars ids-only
Error: Unrecognized flag ('--list-duplicate-vars').
Does anyone has any suggestions?
Thanks in advance for your help,