I'm trying to subset a bgen file to only include a specific list of variants (total of 3516 variants). I've tried using the -incl-variants flag, which looks as follows:
this however creates a bgen file with 0 SNPs in the output.
If I add the option -compare-variants-by rsid, I get more variants than expected (3527). I've been able to see that the extra variants are ones with the same rsid, but a different alleleB.
So I'm wondering if there's a way to filter variants by rsid and alleles?
Thank you, Leda