Plato

Key Features

* Below are some examples of analyses that can be run in PLATO and the options that are available to the user. These examples are intended as a jumping off point for the user to customize their own analyses. For a handy list of all available commands and options, organized by function, see the PLATO Quick Reference, which lists the commands by function and is cross-referenced to their location in the manual. * Recode PED/MAP to Binary PLINK format $ plato load-data --file geno output-bed --file binarygeno * Recode Binary PLINK to PED/MAP, Only a Single Chromosome $ plato load-data --bfile bingeno --chrom 22 \ output-ped --ped geno.ped --map custom_geno.map * Perform a Simple Case/Control GWAS (no covariates, Bonferroni corrected p-values) $ plato load-data --bfile bingeno \ logistic --correction Bonferroni * PheWAS on Quantitative Outcomes using Markers with MAF between 10% and 40% $ plato load-data --bfile bingeno \ load-trait --file pheno.txt --missing=”-999” \ filter-maf --min 0.1 --max 0.4 linear --phewas --covariates AGE,BMI * EWAS (No Genetic Data, Quantitative Predictor Variables) $ plato load-trait --file pheno.txt --dummy-samples --extra-samples logistic --exclude-markers --use-traits --outcome PHENO * Concordance Checking (VCF vs. PED/MAP w/o FID) $ plato load-data --vcf-file data.vcf.gz concordance --file geno --no-fid * GWAS with Dog Data and Permutation Testing $ plato --chroms 38 load-data --file dog_geno logistic --permutations 1000