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, 14:29, 7 August 2013
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| Additional details on [[Rare-Metal#Grouping_from_a_Group_File|groupFile]], [[Rare-Metal#Grouping_from_an_Annotated_VCF_File|annotatedVcf, annotation]] and [[Rare-Metal#Generate_a_VCF_File_to_Annotate_Outside_of_Rare_Metal|writeVcf]] options are available. | | Additional details on [[Rare-Metal#Grouping_from_a_Group_File|groupFile]], [[Rare-Metal#Grouping_from_an_Annotated_VCF_File|annotatedVcf, annotation]] and [[Rare-Metal#Generate_a_VCF_File_to_Annotate_Outside_of_Rare_Metal|writeVcf]] options are available. |
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− | === Sample Size Weighted Meta-analysis === | + | === QC Options === |
− | WEIGHTLABEL [LABEL] (default = 'N') | + | --hwe [hwe.pvalue.cutoff] (default = 1e-05) |
− | PVALUELABEL [LABEL] (default = 'PVALUE') | + | --callRate [variant.call.rate.cutoff] (default = 0.95) |
− | DEFAULTWEIGHT [NUMBER] (default = 1.0)
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− | MINWEIGHT [NUMBER] (default = 1.0)
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| === Inverse Variance Weighted Meta-analysis === | | === Inverse Variance Weighted Meta-analysis === |