RAREMETALWORKER X

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BRIEF DESCRIPTION

RAREMETALWORKER (RMW) supports X-linked markers analysis in both related and unrelated individuals. For related individuals, RMW fits a variance component model with two genetic components (one for autosomes and the other for chromosome X) and a non-shared environment component. When pedigree structure is available, RMW generates separate kinship matrix for chromosome X, besides the kinship matrix generated for autosomes. RMW also supports estimating kinships based on marker genotypes from X chromosome.

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 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:

--xLabel chrX --xStart 2699520 --xEnd 154931044

The default values for these options are --xLabel X --xStart 2699520 --xEnd 154931044. The start and end positions are collected from NCBI genome build 37.

EXAMPLE COMMANDS

Here is an example command to do X-linked associations in related individuals using marker genotypes to estimate the kinships:

./raremetalworker --ped your.ped --dat your.dat --vcf your.vcf.gz --kinGeno --vcX --inverseNormal --makeResiduals --xLabel chrX --xStart 2699520 --xEnd 154931044

Here is an example command to do X-linked associations in related individuals using pedigree structure:

./raremetalworker --ped your.ped --dat your.dat --vcf your.vcf.gz --kinPedigree --vcX  --inverseNormal --makeResiduals --xLabel chrX --xStart 2699520 --xEnd 154931044

Here is an example command to do X-linked associations in unrelated individuals:

./raremetalworker --ped your.ped --dat your.dat --vcf your.vcf.gz --inverseNormal --makeResiduals --xLabel chrX --xStart 2699520 --xEnd 154931044