Chromosome X options


These options facilitate the analysis of genotype data from human chromosome X.

Flag Default Description
-chrX Specifies that this is an analysis of chromosome X data. This flag changes the model parameters by automatically reducing the -Ne value by 25%, and it allows the -g file to include a mixture of dizygous females and hemizygous males.

When using the -chrX option, it is essential to provide a -sample_g file with a column named 'sex', since this tells the program which individuals are males and which are females. More details on the file formats for chromosome X analysis are available here, and you can see an example run here.
-Xpar Specifies that the current dataset comes from a pseudoautosomal region (PAR) of chromosome X, where both males and females are diploid. When used together with -chrX, this flag will reduce -Ne by 25% but otherwise run the analysis in the same way as on the autosomes.