New features:
- LD-matrix computation (--r[2]-unphased)
- --glm qt-residualize mode
- --hwe enhancements for biobank-scale data: support for p-values < 2.23e-308, and sample-size-based thresholds
- --ref-allele/--alt1-allele/--ref-from-fa/--maj-ref support for multiallelic variants
- --check-sex/--impute-sex
Other significant behavior changes relative to alpha 5:
- --allow-extra-chr is never necessary any more
- --set-all-var-ids and related flags are now applied to all --pmerge[-list] inputs
- Polyploid genotypes in VCF/BCF files now default to triggering an error; this behavior is controlled by the --polyploid-mode flag
- -log10(x) column names now consistently start with "NEG_LOG10_", instead of "LOG10_"
- --adjust[-file] QQ column is no longer affected by the 'log10' modifier
- Most computations now consider unknown-sex samples on chrY, unless they explicitly state otherwise