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files

• \*.gid.maf.af.tsv: are files contain gene_id, MAF/kb in 5 major population in 1kG project and AF/kb for each gene(in ENSG_ids)
• \*mapped_snp_af_1k_flank_.tsv: are files that contain MAF, AF for each snps in each one of the five major populations; and the mapped genes based on 1kb flank length. They are source files for use in sum_af_maf.py to generate \*gid.amf.af.tsv files
• gwas_catalog_trait-mappings_r2016-04-24.tsv: exported form GWAS-Catalog. It contains the info how the reported traits are mapped to the mapped traits.
• gwas_catalog_v1.0.1-associations_e84_r2016-04-24.tsv: association file downloaded from GWAS-Catalog website.
• mart_export_gid_gname_37.txt: ENSG_ids and corresponded gene name
• no_of_mapped_trait_sorted.tsv:
• no_of_mapped_trait.tsv: number of mapped traits for each gene name

scripts

• sum_af_maf.py: is a modified version of v2sum_of_maf.py, which is used in calculating MAF/kb and AF/kb.
• af.bash : is used to run sum_af_maf.py in a batch for chromosome 1-22
• af_extraction.py:
• generate_dictfile.bash:
• demo.py:
• add_af_to_file.bash: