This value should be a multiple of the number The -nb-process argument determines how many simultaneous SKAT analyses good_sites file generated by py:mod: genipe,īut additional QC steps could be used to further narrow this list. As an example –covar Age,Hypertension wouldĪdd the Hypertension column as a covariate.Ī list of variants to keep for the analysis is provided here. In our case, we’re only using the Age column, butĪdding covariates is easy. The covariates are provided as a comma separated list of column names from Our case, we are using the quantitative trait SystolicBP representing the The phenotype column is the identifier for the outcome for this analysis. The sample column is the identifier for the column containing sample IDs in Covariates are also included in this file. The phenotype is a tab delimited file containing phenotypic informationįor all the samples. The sample contained the sample identifiers with an ordering consistent This contains the probabilityįor every allele of every variant. The Impute2 file as previously described. They include linear and logistic regression as well as Cox survival Alternative analysis types are presented in other tutorials, but We are calling the program with the skat option to specify the type ofĪnalysis. The line by line explanation of this command is as follows: Imputed-stats skat \ -impute2 data/genipe_is_great.impute2 \ -sample data/genipe_is_great.sample \ -pheno data/phenotypes.txt \ -sample-column Sample \ -pheno-name SystolicBP \ -covar Age \ -extract-sites data/genipe_is_great.good_sites \ -nb-process 4 \ -out my_skat_analysis \ -snp-sets carefully_crafted_snp_sets.txt \ -outcome-type continuous \ Concretely, the expected file looks like this: An optional third field identified by the weight With a single header row containing the following fields: variant, The expected format for SNP sets is very straightforward. Variants according to a biological pathway of interest. Variant prioritization tools to select interesting candidates or to group Possible approaches consist of testing variants in a same gene together, using Describing the currentīest practices to create SNP sets is out of the scope of this tutorial, but True deleterious variants are present in the SNP set. It is also noteworthy that adding neutral variants to a SNP set is generallyĪvoided as much as possible, as it is known to decrease SKAT’s power, even if SKAT is based on the analysis of a “SNP set”.
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