PLINK2 ld analysis

[Ethan Kreuzer]

I was wondering if the "-r2" flag will ever makes its way to plink2. It would be great to have PLINK1.9's ld analysis functionality in PLINK2!

[Christopher Chang]

Eventually, but it is lower-priority than completion of --pmerge-list.

[Mere H]

Hi Dr. Chang,

Under the same topic as Ethan's question, I want to report a software problem for flags on LD pruning in PLINK2. It looks like only "--indep-pairwise" is usable in PLINK2. My institution installed PLINK2 in our institutional high-performance computer platform, but the only LD pruning flag available after the installation is "--indep-pairwise" (See screenshot below). The other flags ( --indep-pairphase, --indep-pairwise, --indep, --indep-order) are not there despite PLINK2 website says they should be available. Our institution's software manager has tried several times, and told me "the other flags may be deprecated".  Could you take a look and see what the problem may be?

Thank you!

Mey

[Christopher Chang]

Thanks for calling this out.  This was actually a typo on the webpage -- I left out a digit in the HTML that was supposed to set --indep / --indep-pairphase to red text.

--indep is low-priority, but I may implement a revised --indep-pairphase (which requires all hardcalls to be phased) soon.