Runs both Genome Wide Association Study (GWAS) and Exome Wide Association Study (EWAS) on VCF format genotype data using 24 different combinations of frequency, function, and relative filters. Used in O'Beirne et al (in review).
Software Dependencies: PLINK https://www.cog-genomics.org/plink2 SnpEff http://snpeff.sourceforge.net/ VCFTools http://vcftools.sourceforge.net/ CADD http://cadd.gs.washington.edu/ R https://cran.r-project.org/ SKAT https://cran.r-project.org/web/packages/SKAT/index.html EMMAX http://genetics.cs.ucla.edu/emmax/ KING http://people.virginia.edu/~wc9c/KING/ Java http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html Python https://www.python.org/download/releases/3.0/ Bgzip/Tabix http://www.htslib.org/download/
Data Dependencies: Input genotype data in VCF format https://samtools.github.io/hts-specs/VCFv4.2.pdf Input phenotype and covariate data in PLINK format https://www.cog-genomics.org/plink/1.9/input#covar 1000 Genomes site list with allele frequency in VCF format. ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz ExAC site list with allele frequency in VCF format. ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/ExAC.r0.3.1.sites.vep.vcf.gz