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* --noeof allows using VCF file without BGZF EOF markers. This is a very rare option to use. If your run is terminated with error message: "", then you might want to check out this option.
* --noeof allows using VCF file without BGZF EOF markers. This is a very rare option to use. If your run is terminated with error message: "", then you might want to check out this option.
=== Output Format===
=== RAREMETAWORKER OUTPUT===
====OUTPUT FILE NAMES====
prefix.traitName.singlevar.score.txt
* Three files are generated automatically by default:
prefix.traitName.singlevar.cov.txt
prefix.traitName.singlevar.score.txt (single variant summary statistics and QC statistics)
prefix.traitName.singlevar.cov.txt (covariance matrices of single variant score statistics)
prefix.singlevar.log (log file)
* If --zip option is used, then the following will be generated automatically:
prefix.traitName.singlevar.score.txt.gz
prefix.traitName.singlevar.cov.txt.gz
prefix.singlevar.log
prefix.singlevar.log
* prefix.traitName.singlevar.score.txt contains summary statistics that are needed by Rare-Metal. An example is shown in below:
* If --recessive and/or --dominant options are used, then the following files are also generated '''in addition''' to the above files
prefix.traitName.recessive.singlevar.score.txt.gz
prefix.traitName.recessive.singlevar.cov.txt.gz
prefix.traitName.dominant.singlevar.score.txt.gz
prefix.traitName.dominant.singlevar.cov.txt.gz
* If --kinGeno --kinSave is used, then the genomic relationship matrix is stored in
prefix.Empirical.Kinship.gz
* If --vcX option is used, then the genomic relationship matrix from chromosome X is stored in
prefix.Empirical.KinshipX.gz
====OUTPUT FILE FORMATS====
* In the file with summary statistics named 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
