Changes

* If you want to use a linear mixed model approach to correct family structure, population structure, or cryptic relatedness, you should issue --vcX option in your command line. This approach will fit a separate linear mixed model using both autosomal kinship matrix and chromosomeX kinship matrix. This approach is believed to have larger power with type I error well controlled.

* If you want to use a linear mixed model approach to correct family structure, population structure, or cryptic relatedness, you should issue --vcX option in your command line. This approach will fit a separate linear mixed model using both autosomal kinship matrix and chromosomeX kinship matrix. This approach is believed to have larger power with type I error well controlled.

* On the other hand, if you want a fast association for chromosome X, another valid approach is to issue --vcX --separateX options. This will initiate fitting a separate linear mixed model using chromosomeX kinship only for analyzing markers on chromosomeX. This approach is expected to be faster than the above option, but with less power, although type I error is also expected to be under control.

* On the other hand, if you want a fast association for chromosome X, another valid approach is to issue --vcX --separateX options. This will initiate fitting a separate linear mixed model using chromosomeX kinship only for analyzing markers on chromosomeX. This approach is expected to be faster than the above option, but with less power, although type I error is also expected to be under control.

* Male genotypes for variants in nonPAR region are coded to be 0 or 2. If a male is heterozygous in nonPAR region, then the genotype of that male sample is considered missing and will be imputed using mean genotype.

* Male genotypes for variants in nonPAR region are coded to be 0 or 2.  

* If a male is heterozygous in nonPAR region, then the genotype of that male sample is considered missing and will be imputed using mean genotype.

* If a male has genotype coded as ./x in nonPAR region, then the genotype of that male sample is considered missing and will be imputed using mean genotype.