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FAVOR Full Database

Harvard Dataverse (Africa Rice Center, Bioversity International, CCAFS, CIAT, IFPRI, IRRI and WorldFish)

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Title FAVOR Full Database
 
Identifier https://doi.org/10.7910/DVN/KFUBKG
 
Creator Zhou, Hufeng
Arapoglou, Theodore
Li, Xihao
Li, Zilin
Lin, Xihong
 
Publisher Harvard Dataverse
 
Description Functional Annotation of Variants - Online Resource (FAVOR, https://favor.genohub.org) is a comprehensive whole genome variant annotation database and a variant browser, providing hundreds of functional annotation scores from a variety of aspects of variant biological function. This FAVOR Full Database is comprised of a collection of full annotation scores for all possible SNVs (8,812,917,339) and observed indels (79,997,898) in Build GRCh38/hg38, including
VARIANT INFO, CHROMOSOME, POSITION, REFERENCE ALLELE, ALTERNATIVE ALLELE, VARIANT-ANNOVAR, CHROMOSOME, START-POSITION, END-POSITION, REF-ANNOVAR, ALT-ANNOVAR, POSITION, REF-VCF, ALT-VCF, ALOFT-VALUE, ALOFT-DESCRIPTION, APC-CONSERVATION, APC-CONSERVATION-V2, APC-EPIGENETICS-ACTIVE, APC-EPIGENETICS, APC-EPIGENETICS-REPRESSED, APC-EPIGENETICS-TRANSCRIPTION, APC-LOCAL-NUCLEOTIDE-DIVERSITY, APC-LOCAL-NUCLEOTIDE-DIVERSITY-V2, APC-LOCAL-NUCLEOTIDE-DIVERSITY-V3, APC-MAPPABILITY, APC-MICRO-RNA, APC-MUTATION-DENSITY, APC-PROTEIN-FUNCTION, APC-PROTEIN-FUNCTION-V2, APC-PROTEIN-FUNCTION-V3, APC-PROXIMITY-TO-CODING, APC-PROXIMITY-TO-CODING-V2, APC-PROXIMITY-TO-TSSTES, APC-TRANSCRIPTION-FACTOR, BRAVO-AN, BRAVO-AF, FILTER-STATUS, CAGE-ENHANCER, CAGE-PROMOTER, CAGE-TC, CLNSIG, CLNSIGINCL, CLNDN, CLNDNINCL, CLNREVSTAT, ORIGIN, CLNDISDB, CLNDISDBINCL, GENEINFO, POLYPHEN2-HDIV-SCORE, POLYPHEN2-HVAR-SCORE, MUTATION-TASTER-SCORE, MUTATION-ASSESSOR-SCORE, METASVM-PRED, FATHMM-XF, FUNSEQ-VALUE, FUNSEQ-DESCRIPTION, GENECODE-COMPREHENSIVE-CATEGORY, GENECODE-COMPREHENSIVE-INFO, GENECODE-COMPREHENSIVE-EXONIC-CATEGORY, GENECODE-COMPREHENSIVE-EXONIC-INFO, GENEHANCER, AF-TOTAL, AF-ASJ-FEMALE, AF-EAS-FEMALE, AF-AFR-MALE, AF-FEMALE, AF-FIN-MALE, AF-OTH-FEMALE, AF-AMI, AF-OTH, AF-MALE, AF-AMI-FEMALE, AF-AFR, AF-EAS-MALE, AF-SAS, AF-NFE-FEMALE, AF-ASJ-MALE, AF-RAW, AF-OTH-MALE, AF-NFE-MALE, AF-ASJ, AF-AMR-MALE, AF-AMR-FEMALE, AF-SAS-FEMALE, AF-FIN, AF-AFR-FEMALE, AF-SAS-MALE, AF-AMR, AF-NFE, AF-EAS, AF-AMI-MALE, AF-FIN-FEMALE, LINSIGHT, GC, CPG, MIN-DIST-TSS, MIN-DIST-TSE, SIFT-CAT, SIFT-VAL, POLYPHEN-CAT, POLYPHEN-VAL, PRIPHCONS, MAMPHCONS, VERPHCONS, PRIPHYLOP, MAMPHYLOP, VERPHYLOP, BSTATISTIC, CHMM-E1, CHMM-E2, CHMM-E3, CHMM-E4, CHMM-E5, CHMM-E6, CHMM-E7, CHMM-E8, CHMM-E9, CHMM-E10, CHMM-E11, CHMM-E12, CHMM-E13, CHMM-E14, CHMM-E15, CHMM-E16, CHMM-E17, CHMM-E18, CHMM-E19, CHMM-E20, CHMM-E21, CHMM-E22, CHMM-E23, CHMM-E24, CHMM-E25, GERP-RS, GERP-RS-PVAL, GERP-N, GERP-S, ENCODEH3K4ME1-SUM, ENCODEH3K4ME2-SUM, ENCODEH3K4ME3-SUM, ENCODEH3K9AC-SUM, ENCODEH3K9ME3-SUM, ENCODEH3K27AC-SUM, ENCODEH3K27ME3-SUM, ENCODEH3K36ME3-SUM, ENCODEH3K79ME2-SUM, ENCODEH4K20ME1-SUM, ENCODEH2AFZ-SUM, ENCODE-DNASE-SUM, ENCODETOTAL-RNA-SUM, GRANTHAM, FREQ100BP, RARE100BP, SNGL100BP, FREQ1000BP, RARE1000BP, SNGL1000BP, FREQ10000BP, RARE10000BP, SNGL10000BP, REMAP-OVERLAP-TF, REMAP-OVERLAP-CL, CADD-RAWSCORE, CADD-PHRED, K24-BISMAP, K24-UMAP, K36-BISMAP, K36-UMAP, K50-BISMAP, K50-UMAP, K100-BISMAP, K100-UMAP, NUCDIV, RDHS, RECOMBINATION-RATE, REFSEQ-CATEGORY, REFSEQ-INFO, REFSEQ-EXONIC-CATEGORY, REFSEQ-EXONIC-INFO, SUPER-ENHANCER, TG-AFR, TG-ALL, TG-AMR, TG-EAS, TG-EUR, TG-SAS, UCSC-CATEGORY, UCSC-INFO, UCSC-EXONIC-CATEGORY, UCSC-EXONIC-INFO.

These annotation scores can be integrated into FAVORannotator (https://github.com/zhouhufeng/FAVORannotator) to create an annotated GDS (aGDS) file by storing the genotype data and their functional annotation data in an all-in-one file. The aGDS file can then facilitate a wide range of functionally-informed downstream analyses.
 
Subject Computer and Information Science
Medicine, Health and Life Sciences
Functional Annotation
 
Contributor Zhou, Hufeng