ANNOVAR Documentation

ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform:

Please click the menu items to navigate through this website. To recieve program updates, please use the ANNOVAR mailing list. If you have questions, comments and bug reports, please post them in the Disqus comment form in this website (or email me directly). Thank you very much for your help and support!

new 2018Dec04: The ABRAOM score (Brazilian genomic variants) is updated (~1000 lines in previous version do not have abraom_cegh_filter).

new 2018Dec03: The MCAP score v1.3 is available for hg19 coordinate (use mcap13 keyword to download).

2018Nov19: ANNOVAR is back online and all databases should be available now. Please report any problem that you encounter.

2018Nov15: ANNOVAR (downdb function to download databases) is temporarily down and we are finding replacement servers at the moment. Please check back to the page for updates.

new 2018Oct23: The non-commercial dbSNFP scores in ANNOVAR is updated to version 3.5c (use dbnsfp35c to download).

new 2018Sep20: The dbSNFP scores in ANNOVAR is updated to version 3.5a (use dbnsfp35a to download). The regsnpintron database is updated to fix problems in certain lines of the file.

new 2018Jul08: ClinVar version 20180603 is available for use in ANNOVAR, with slight format changes compared to previous versions. Note that users are advised to use to make your own ClinVar databases for use in ANNOVAR (see details here, so you do not need to wait for me to update.

new 2018Apr16: ANNOVAR new version is available now! You can use the old link to download, or you can register again to get download email. This release contins some minor fixes and improvements.

new 2018Mar25: pre-computed intervar scores (version 20180118) is available on both hg19 and hg38 now with intervar_20180118 keyword. Only missense variants are included, and this is meant for a quick-and-dirty analysis of most missense variants. For a more comprehensive/formal calculation of scores, download instead.

new 2018Mar02: About 2.4 million Brazilian genomic variants with allele frequencies are available now in hg19/hg38 coordinate. The data set comprises exomic variants of 609 elderly individuals from a census-based sample from the city of São Paulo. Please use abraom as the keyword to download and annotate, and refer to the original publication for details.

new 2017Oct03: Latest clinvar (20170905) is available now through ANNOVAR in hg19 and hg38 coordinates. A long-standing problem on multi-allelic variants in ClinVar is now addressed, so that multi-allelic variants are now correctly assigned to the corresponding benign/pathogenic categories. The 20170130/20170501 versions are also updated to resolve this issue.

new 2017Sep29: avsnp150 is available through ANNOVAR now in hg19 and hg38 coordinate, to annotate your variants with dbSNP identifiers.

new 2017Sep12: Per user request, we have now made hg38 version of ensGene available through ANNOVAR directly so that users do not need to build it themselves.

new 2017Jul16: ANNOVAR new version is available now! You can use the old link to download, or you can register again to get download email. This release contins some minor fixes and improvements: fixed a bug in calculating upstream distance that print when -separate is specified in, improvements to to report more stopgain/stoploss and fix use-of-uninitialized-value issue, slight change to to handle mal-formed VCF file.

new 2017Jun01: ANNOVAR new version is available now! You can use the old link to download, or you can register again to get download email. Important features include: gx operation is added in table_annovar so that xref information for genes (such as gene-disease relationships) can be included (see quick start-up for examples), show complete amino acid change (such as c.35delG:p.G12Vfs*2) in gene annotaion in and with -polish argument, upstream variants now show distance to transcriptional start, splice variants at UTR now shows details, etc. (Update 2017Jun08: some users complained about format change in 2017jun01 version of table_annovar, where semicolon was used instead of comma for gene-based annotation, we have now reverted this change. Additional feature for -xreffile with multiple annotation columns has been implemented. Please re-download the code)

new 2017Jun01: Updated refGene, knownGene, ensGene definition and FASTA file on hg18/hg19/hg38 coordinates are available to download with -webfrom annovar argument. However, users can always build the latest version yourself.

new 2017May16: Updated instructions on how to handle noncoding variants in COSMIC version 81 here.

new 2017Mar11: gnomAD collection is available at ANNOVAR now, for both hg19 and hg38 coordinates. Use keyword gnomad_exome and gnomad_genome to download and use them.

new 2017Feb21: dbNSFP3.3a is updated for hg18/hg19/hg38 now. We now added the rankscore for each scoring system, and for variants with multiple prediction scores, only the most deleterious (rather than highest) scores are kept.

new 2017Feb15: Clinvar version 20170130 is available for hg19/hg38 now in ANNOVAR with keyword clinvar_20170130 to download.

new 2017Feb02: InterVar automated prediction is available for clinical interpretation of missense variants, with 18 criteria based on 2015 ACMG-AMP guidelines. Use intervar_20170202 keyword to download and use. Read the InterVar paper for details.

new 2017Jan24: dbNSFP version 3.3a is available on hg18, hg19 and hg38 in ANNOVAR, with whole-exome SIFT, PolyPhen2 HDIV, PolyPhen2 HVAR, LRT, MutationTaster, MutationAssessor, FATHMM, PROVEAN, MetaSVM, MetaLR, VEST, M-CAP, CADD, GERP++, DANN, fathmm-MKL, Eigen, GenoCanyon, fitCons, PhyloP and SiPhy scores.

new 2017Jan23: cadd13 (CADD version 1.3), cadd13gt10, cadd13gt20 are slightly updated to fix a format problem with contigs that are not placed on chromosomes.

new 2016Dec05: REVEL (Rare Exome Variant Ensemble Learner) scores for hg19 and hg38 are available from ANNOVAR now with revel keyword.

new 2016Nov04: M-CAP (Mendelian Clinically Applicable Pathogenicity) scores for hg19 and hg38 are available from ANNOVAR now with mcap keyword.

new 2016Oct24: GME (Greater Middle East Variome) is available to download from ANNOVAR now with keyword gme. It contains allele frequency data on NWA (northwest Africa), NEA (northeast Africa), AP (Arabian peninsula), Israel, SD (Syrian desert), TP (Turkish peninsula) and CA (Central Asia).

new 2016Jun22: icgc21 (International Cancer Genome Consortium version 21), cadd13, cadd13gt10, cadd13gt20 (CADD version 1.3) is available to download from ANNOVAR now.

new 2016Jun06: avsnp147 (hg19 and hg38), which is a modified version of dbSNP with left-normalization and allelic splitting, is available to download from ANNOVAR now.

new 2016Apr23: Slightly updated ExAC03 non-TCGA and non-psych datasets are available with modified headers.

new 2016Mar30: Whole-genome Eigen scores are available in ANNOVAR, which uses a spectral approach integrating functional genomic annotations for coding and noncoding variants. See here for detailed instructions. User contributed SNP database for Indian populations is available in Download page.

new 2016Mar15: Updated whole-genome FATHMM-MKL scores are available, which fixed an error that coding/noncoding scores were reversed.

new 2016Feb01: A user pointed out a bug when more than 6 threads are used in multi-threaded gene-based annotation. This bug was fixed and you can now re-download the ANNOVAR package.

new 2016Jan23: The mitimpact24 (version 2.4) database is made available in ANNOVAR now. It provides effect prediction of mitochondrial variants.