Beta 1 build posted

[Christopher Chang]

The PLINK 1.90 beta 1 build has been posted.  Features added over the last seven months include:

* VCF/BCF2 (--vcf, --bcf) and Oxford-format (--data, --bgen) data import.

* Accelerated --fast-epistasis test and --r2 matrix computation.

* Optional mid-p adjustments for Hardy-Weinberg equilibrium and Fisher's exact tests.

* --split-x and --merge-x flags to simplify handling of the XY pseudoautosomal region.

* Support for a moderate number (up to ~2500) of unplaced contigs.

* A simple PCA implementation (--pca).

* Accelerated --blocks haploblock caller, supporting all of Haploview's options.

* A faster logistic regression algorithm, obtained via crowdsourcing.

The website now has a list of unsupported PLINK 1.07 (documented) flags, which will be updated as development continues.  (If you're actively using something in that list, you're welcome to drop us a note; we'll try to reimplement it sooner rather than later.)