#Installation
This code was developed to calculate Meta-EA score for a given gene in a Linux system where perl is installed.
STEPS:
1. Create an installation directory
2. Copy the MetaEA_submit_to_NatComm.pl to the installation directory 
3. Copy the code directory, including the pred_average.pl  pred_average_with_EA.pl  score_file2cov_file.pl files to the installation directory 

#Running MetaEA_submit_to_NatComm.pl
STEPS:
1. Create a directory for the gene of interest inside the installation folder and name it as the gene identifier (say GENE_ID) 
2. Collect the prediction scores of the reference method and store it as a tab-separated file inside the gene directory, named as GENE_ID.EA
3. Collect the prediction scores of as many of the predefined component methods and store them as a tab-separated files inside the gene directory. 
The code will look for:
GENE_ID.CADD_raw_dbNSFP4.0a
GENE_ID.CADD_raw-v1.2_dbNSFP2.9.1
GENE_ID.CADD_raw-v1.3_dbNSFP3.5a
GENE_ID.DANN_dbNSFP4.0a
GENE_ID.DEOGEN2_dbNSFP4.0a
GENE_ID.Eigen-PC-raw_dbNSFP4.0a
GENE_ID.Eigen-raw_dbNSFP4.0a
GENE_ID.FATHMM_dbNSFP4.0a
GENE_ID.fathmm-MKL_dbNSFP4.0a
GENE_ID.fathmm-XF_dbNSFP4.0a
GENE_ID.GenoCanyon_dbNSFP4.0a
GENE_ID.GM12878_fitCons_dbNSFP4.0a
GENE_ID.H1-hESC_fitCons_dbNSFP4.0a
GENE_ID.HUVEC_fitCons_dbNSFP4.0a
GENE_ID.integrated_fitCons_dbNSFP4.0a
GENE_ID.LRT_dbNSFP4.0a
GENE_ID.M-CAP_dbNSFP4.0a
GENE_ID.M-CAP-v1.0_dbNSFP3.5a
GENE_ID.MetaLR_dbNSFP4.0a
GENE_ID.MetaSVM_dbNSFP4.0a
GENE_ID.MPC_dbNSFP4.0a
GENE_ID.MutationAssessor_dbNSFP4.0a
GENE_ID.MutationTaster_dbNSFP4.0a
GENE_ID.MutationTaster-v1_dbNSFP2.9.1
GENE_ID.MutPred_dbNSFP4.0a
GENE_ID.MVP_dbNSFP4.0a
GENE_ID.Polyphen2_HDIV_dbNSFP4.0a
GENE_ID.Polyphen2_HVAR_dbNSFP4.0a
GENE_ID.PrimateAI_dbNSFP4.0a
GENE_ID.PROVEAN_dbNSFP4.0a
GENE_ID.REVEL_dbNSFP4.0a
GENE_ID.SIFT4G_dbNSFP4.0a
GENE_ID.SIFT_dbNSFP4.0a
GENE_ID.SIFT-same_dbNSFP2.9.1
GENE_ID.VEST3_dbNSFP3.5a
GENE_ID.VEST4_dbNSFP4.0a
Additional methods can be added with appropriate editing of the  MetaEA_submit_to_NatComm.pl file
In each predicting method file, the first column should show the variant (e.g. D2N) and the last column should be the rank score (e.g. 0.6009) between 0 (benign) and 1 (pathogenic). 

4. outcome will be a file GENE_ID.MetaEA that contains the Meta-EA scores. 

