Changes

==SOFTWARE SPECS==

==SOFTWARE SPECS==

RMW takes male genotype to be 0 or 2. This means that whenever an alternative allele is observed in male on chromosome X (non-PAR region), it is considered to have the same effect as a female with homozygous alternative alleles. In the VCF file, male genotypes must be coded in the format of 1/1, 0/0, or be coded to be haploids as 0 or 1. Any variant with male genotypes stored as heterozygous (e.g. 0/1) in this region is skipped from the analysis.  

RMW takes male genotype to be 0 or 2. This means that whenever an alternative allele is observed in male on chromosome X (non-PAR region), it is considered to have the same effect as a female with homozygous alternative alleles. In the VCF file, male genotypes must be coded in the format of 1/1, 0/0, or be coded to be haploids as 0 or 1. Any heterozygous male genotypes are treated as missing and imputed to the mean.  

The label of chromosome X can be changed flexibly according to the entry in VCF file using --xLabel option. The non-PAR region can also be specified using --xStart and --xEnd options. Then RMW can automatically differentiate between the PAR and non-PAR region on Chromosome X and decode male genotype accordingly. For example, if the X chromosome in the VCF file is labeled as “chrX”, then adding the following options lets RMW recognize variants with CHR=”chrX” and 2699520 ≤POS≤154931044 for chromosome X associations:

The label of chromosome X can be changed flexibly according to the entry in VCF file using --xLabel option. The non-PAR region can also be specified using --xStart and --xEnd options. Then RMW can automatically differentiate between the PAR and non-PAR region on Chromosome X and decode male genotype accordingly. For example, if the X chromosome in the VCF file is labeled as “chrX”, then adding the following options lets RMW recognize variants with CHR=”chrX” and 2699520 ≤POS≤154931044 for chromosome X associations: