A future release of haptools will add support for repeats in the ld command. Unfortunately, that will very likely require us to make breaking changes to the ld command to make the interface flexible enough for users to be able to specify all of the possible ways to compute LD with a repeat or a set of repeats. So for now, we will just delay the breaking changes and explicitly ignore repeats in the meantime.
Users who are interested in computing LD with repeats may use the haptools API or PLINK2's --ld dosage feature until we add support.
A future release of haptools will add support for repeats in the
ldcommand. Unfortunately, that will very likely require us to make breaking changes to theldcommand to make the interface flexible enough for users to be able to specify all of the possible ways to compute LD with a repeat or a set of repeats. So for now, we will just delay the breaking changes and explicitly ignore repeats in the meantime.Users who are interested in computing LD with repeats may use the haptools API or PLINK2's
--ld dosagefeature until we add support.