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Rare-Metal-Worker has the following features:
Rare-Metal-Worker has the following features:
* Takes genotypes from either PED file or VCF file.
* Takes genotypes from either PED file or VCF file.
* Generates summary level statistics for both related and unrelated individuals.
* Generates summary statistics for both related and unrelated individuals.
* Generates linkage disequilibrium matrices summarizing covariance between single marker statistics using an adjustable sliding window.
* Generates linkage disequilibrium matrices summarizing covariance between single marker statistics using an adjustable sliding window.
* Optionally handles related individuals using a kinship matrix derived from either pedigree or genotype data.
* Optionally handles related individuals using a kinship matrix derived from either pedigree or genotype data.
prefix.traitName.singlevar.cov.txt
prefix.traitName.singlevar.cov.txt
* prefix.traitName.singlevar.score.txt contains summary level statistics that are needed by Rare-Metal. An example is shown in below:
* prefix.traitName.singlevar.score.txt contains summary statistics that are needed by Rare-Metal. An example is shown in below:
LDL mean= -0.00, variance= 1.00, heritability= 34.30
LDL mean= -0.00, variance= 1.00, heritability= 34.30
