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=== Running EMMAX with dosages ===
=== Running EMMAX with dosages ===
If you add -Z option, it will accept .tped file format, where each individual is represented as one dosage value (ranging from 0 to 2), instead of two genotype columns, (which is one of the standard PLINK dosage format). You will be able to run EMMAX with this model. But when creating the kinship matrix, you will not be able to use dosage-based genotypes.
If you add -Z option, it will accept .tped file format, where each individual is represented as one dosage value (ranging from 0 to 2), instead of two genotype columns, (which is one of the standard PLINK dosage format). You will be able to run EMMAX with this model. But when creating the kinship matrix, you will not be able to use dosage-based genotypes.
== Frequently asked Questions ==
=== Effect allele ==
Q. Which allele is effect allele?
A. EMMAX simply follows the encoding scheme of .tped file in additive model. So whichever allele encoded as 1 in the .tped file, it will be the effect allele (usually the major allele)
=== Support for VCF format and Gene-level Burden Test ===
=== Support for VCF format and Gene-level Burden Test ===
Use [[EPACTS]] software pipeline for running EMMAX with VCF files, including the implementations of gene-level burden tests.
Q. Is there a version supporting VCF format and gene-level burden test?
A. Use [[EPACTS]] software pipeline for running EMMAX with VCF files, including the implementations of gene-level burden tests.
== Acknowledgements ==
== Acknowledgements ==
This research was supported by National Science Foundation grants 0513612, 0731455 and 0729049, and National Institutes of Health (NIH) grants 1K25HL080079 and U01-DA024417. N.A.Z. is supported by the Microsoft Research Fellowship. H.M.K. is supported by the Samsung Scholarship, National Human Genome Research Institute grant HG00521401, National Institute for Mental Health grant NH084698 and GlaxoSmithKline. C.S. is partially supported by NIH grants GM053275-14, HL087679-01, P30 1MH083268, 5PL1NS062410-03, 5UL1DE019580-03 and 5RL1MH083268-03. N.B.F. and S.K.S. are supported by NIH grants HL087679-03, 5PL1NS062410-03, 5UL1DE019580-03 and 5RL1MH083268-03. This research was supported in part by the University of California, Los Angeles subcontract of contract N01-ES-45530 from the National Toxicology Program and National Institute of Environmental Health Sciences to Perlegen Sciences.
This research was supported by National Science Foundation grants 0513612, 0731455 and 0729049, and National Institutes of Health (NIH) grants 1K25HL080079 and U01-DA024417. N.A.Z. is supported by the Microsoft Research Fellowship. H.M.K. is supported by the Samsung Scholarship, National Human Genome Research Institute grant HG00521401, National Institute for Mental Health grant NH084698 and GlaxoSmithKline. C.S. is partially supported by NIH grants GM053275-14, HL087679-01, P30 1MH083268, 5PL1NS062410-03, 5UL1DE019580-03 and 5RL1MH083268-03. N.B.F. and S.K.S. are supported by NIH grants HL087679-03, 5PL1NS062410-03, 5UL1DE019580-03 and 5RL1MH083268-03. This research was supported in part by the University of California, Los Angeles subcontract of contract N01-ES-45530 from the National Toxicology Program and National Institute of Environmental Health Sciences to Perlegen Sciences.
