1,555
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchMinor typos fixed
'''Rare-Metal-Worker''' is a software for generating summary level statistics for meta analyses using Rare-Metals. It handles both related individuals and unrelated individuals.
'''Rare-Metal-Worker''' is a tool for generating summary level statistics for rare variant and gene level meta analyses using Rare-Metal. It handles both related individuals and unrelated individuals.
== Change Log ==
== Change Log ==
* Takes genotypes from either Merlin format PED file or VCF file.
* Takes genotypes from either Merlin format PED file or VCF file.
* Generates summary level statistics for both related and unrelated individuals.
* Generates summary level statistics for both related and unrelated individuals.
* Generates variants LD matrix by a sliding window of preferred size.
* Generates linkage disequilibrium matrices summarizing covariance between single marker statistics using an adjustable sliding window.
* Handles related individuals using a kinship matrix derived from the pedigree or from genotype data.
* Optionally handles related individuals using a kinship matrix derived from either pedigree or genotype data.
* Has the option of fitting shared environment.
* Has the option of fitting shared environment.
* Can handle variants on Chromosome X.
* Can handle variants on Chromosome X.
=== Download ===
=== Download ===
* The package can be downloaded here:
* The source package for Linux and Mac can be downloaded here:
http://genome.sph.umich.edu/wiki/File:RareMetalWorker.0.0.1.tgz
http://genome.sph.umich.edu/wiki/File:RareMetalWorker.0.0.1.tgz
=== Input Files ===
=== Input Files ===
Rare-Metal-Worker needs the following files as input: PED and DAT file in Merlin format, '''AND/OR''' a VCF file. When genotypes are stored in PED and DAT file, VCF file is not needed. However, even if genotypes are saved in a VCF file, PED and DAT files are still needed for carrying covariate and trait information.
Rare-Metal-Worker needs the following files as input: PED and DAT file in Merlin format, '''AND/OR''' a VCF file. When genotypes are stored in PED and DAT file, the VCF file is not needed. However, even if genotypes are saved in a VCF file, PED and DAT files are still needed for carrying covariate and trait information.
==== PED and DAT Files ====
==== PED and DAT Files ====
* When PED file has genotypes saved, there is no need of VCF file as input.
* When PED file has genotypes saved, there is no need for a VCF file as input.
* Rare-Metal-Worker takes PED and DAT file in Merlin format. Please refer to the following link for specifications.
* Rare-Metal-Worker takes PED and DAT file in Merlin format. Please refer to the following link for specifications.
http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html
http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html
Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044]
Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044]
Usage for these options is detailed below.
==== Input Files ====
==== Input Files ====
* When genotypes are saved in VCF file, PED and DAT files are also necessary for containing pedigree structure, covariate and trait information. An example is in the following:
* When genotypes are saved in a VCF file, PED and DAT files are used for specifying pedigree structure, covariate and trait information. An example command line might look like this:
--ped input.ped --dat input.dat --vcf input.vcf.gz
--ped input.ped --dat input.dat --vcf input.vcf.gz
* When genotypes are saved in PED file, VCF file is not needed. An example is in the following:
* When genotypes are saved in the PED file, the VCF file is not needed. An example command line might look like this:
--ped input.ped --dat input.dat
--ped input.ped --dat input.dat
==== VC Options ====
==== VC Options ====
* When --vcShared and --vcX are specified, Rare-Metal-Worker know that you want to fit shared environment and/or chromosome X variance component together with genetic component and non-shared environment.
* When --vcShared and --vcX are specified, Rare-Metal-Worker knows that you want to fit shared environment and/or chromosome X variance component together with genetic component and non-shared environment.
* When --useCovariates is specified, Rare-Metal-Worker understands covariates should be read from PED file. Covariates are fit as fixed effects.
* When --useCovariates is specified, Rare-Metal-Worker understands covariates should be read from PED file. Covariates are modeled as fixed effects.
==== Trait Options ====
==== Trait Options ====
* --makeResiduals is created to be used with --useCovariates together to generate residuals from linear regressions ignoring variance components first and then variance components will be estimated from those residuals. If --inverseNormal options is also used, then the residuals from linear regression will be inverse normalized before fitting variance component model.
* --makeResiduals can be combined with --useCovariates to generate residuals from a simple linear regressions before analysis. If the --inverseNormal option is also used, then the residuals will be quantile normalized before fitting variance component model.
** An example to use residuals after adjusting covariates, inverse normalize the residuals and then fit variance component model is in the following:
** An example Command line requesting pre-adjustment for covariates before fitting a variance component follows:
--useCovariates --makeResiduals --inverseNormal
--useCovariates --makeResiduals --inverseNormal
** An example to fit fixed effects together with variance components is in the following:
** An example command line requesting joint modeling of fixed effects and variance components follows:
--useCovariates --inverseNormal
--useCovariates --inverseNormal
* If --inverseNormal is used WITHOUT --makeResiduals, then trait values are inverse normalized before any model fitting.
* If --inverseNormal is used WITHOUT --makeResiduals, then trait values are inverse normalized before any model fitting.
