ANNOVAR main package

Please join the ANNOVAR mailing list at google groups here to receive announcements on software updates.

The latest version of ANNOVAR (2015Mar22) can be downloaded here (registration required).

ANNOVAR is written in Perl and can be run as a standalone application on diverse hardware systems where standard Perl modules are installed.

Additional databases

Many of the databases that ANNOVAR uses can be directly retrieved from UCSC Genome Browser Annotation Database by -downdb argument.

Several very commonly used annotation databases for human genomes are additionally provided below. In general, users can use -downdb -webfrom annovar in ANNOVAR directly to download these databases.

- For gene-based annotation

Build Table Name Explanation Date
hg18 refGene FASTA sequences for all annotated transcripts in RefSeq Gene 20150322
hg19 refGene same as above 20150322
hg38 refGene save as above 20150322
hg18 knownGene FASTA sequences for all annotated transcripts in UCSC Known Gene 20150322
hg19 knownGene same as above 20150322
hg38 knownGene same as above 20150322
hg18 ensGene FASTA sequences for all annotated transcripts in ENSEMBL Gene 20150322
hg19 ensGene same as above 20150322

- For filter-based annotation

Build Table Name Explanation Date
hg18 avsift whole-exome SIFT scores for non-synonymous variants (obselete and should not be uesd any more) 20120222
hg19 avsift same as above 20120222
hg19 avsnp138 dbSNP138 with allelic splitting and left-normalization 20141223
hg19 avsnp142 dbSNP142 with allelic splitting and left-normalization 20141228
hg18 ljb_sift whole-exome LJBSIFT scores (1-SIFT!) 20120222
hg19 ljb_sift same as above 20120222
hg18 ljb2_sift whole-exome SIFT scores (version 2) 20130621
hg19 ljb2_sift same as above 20130621
hg18 ljb23_sift whole-exome SIFT scores with missing values imputed 20140222
hg19 ljb23_sift same as above 20140222
hg18 ljb26_sift whole-exome SIFT scores with missing values imputed 20140925
hg19 ljb26_sift samea s above 20140925
hg18 ljb_pp2 whole-exome PolyPhen scores 20120222
hg19 ljb_pp2 same as above 20120222
hg18 ljb2_pp2hdiv whole-exome PolyPhen scores built on HumanDiv database (for complex phenotypes) 20130621
hg19 ljb2_pp2hdiv same as above 20120222
hg18 ljb23_pp2hdiv whole-exome PolyPhen 2 scores built on HumanDiv database (for complex phenotypes) 20140222
hg19 ljb23_pp2hdiv same as above 20140222
hg18 ljb26_pp2hdiv same as above 20140925
hg19 ljb26_pp2hdiv same as above 20140925
hg18 ljb2_pp2hvar whole-exome PolyPhen version 2 scores built on HumanVar database (for Mendelian phenotypes) 20130621
hg19 ljb2_pp2hvar same as above 20130621
hg18 ljb23_pp2hvar whole-exome PolyPhen 2 scores built on HumanVar database (for Mendelian phenotypes) 20140222
hg19 ljb23_pp2hvar same as above 20140222
hg19 ljb26_pp2hvar same as above 20140925
hg19 ljb26_pp2hvar same as above 20140925
hg18 ljb26_cadd whole-exome CADD scores, including raw score and categorical prediction 20140915
hg18 ljb_phylop whole-exome PhyloP scores 20120222
hg19 ljb_phylop same as above 20120222
hg18 ljb2_phylop whole-exome PhyloP scores 20130621
hg19 ljb2_phylop same as above 20130621
hg18 ljb23_phylop whole-exome PhyloP scores 20140222
hg19 ljb23_phylop same as above 20140222
hg18 ljb26_phylop46way_placental whole-exome PhyloP scores based on 46-way alignment placental subset 20140925
hg19 ljb26_phylop46way_placental same as above 20140925
hg18 ljb26_phylop100way_vertebrate whole-exome PhyloP scores based on 100-way alignment vertebrate subset 20140925
hg19 ljb26_phylop100way_vertebrate same as above 20140925
hg18 ljb_lrt whole-exome LRT scores 20120222
hg19 ljb_lrt same as above 20120222
hg18 ljb2_lrt whole-exome LRT scores (version 2) 20130621
hg19 ljb2_lrt same as above 20130621
hg18 ljb23_lrt whole-exome LRT scores 20140222
hg19 ljb23_lrt same as above 20140222
hg18 ljb26_lrt whole-exome LRT scores 20140915
hg19 ljb26_lrt same as above 20140915
hg18 ljb_mt whole-exome MutationTaster scores 20120222
hg19 ljb_mt same as above 20120222
hg18 ljb2_mt whole-exome MutationTaster scores 20130621
hg19 ljb2_mt same as above 20130621
hg18 ljb23_mt whole-exome MutationTaster scores 20140222
hg19 ljb23_mt same as above 20140222
hg18 ljb26_mt whole-exome MutationTaster scores 20140925
hg19 ljb26_mt same as above 20140925
hg18 ljb2_ma whole-exome MutationAssessor scores 20130621
hg19 ljb2_ma same as above 20140915
hg18 ljb23_ma whole-exome MutationAssessor scores 20140222
hg19 ljb23_ma same as above 20140222
hg18 ljb26_ma whole-exome MutationAssessor scores 20140925
hg19 ljb26_ma same as above 20140925
hg18 ljb2_fathmm whole-exome FATHMM scores 20130621
hg19 ljb2_fathmm same as above 20130621
hg18 ljb23_fathmm whole-exome FATHMM scores 20140222
hg19 ljb23_fathmm same as above 20140222
hg18 ljb26_fathmm whole-exome FATHMM scores 20140925
hg19 ljb26_fathmm same as above 20140925
hg18 ljb2_siphy whole-exome SiPhy scores 20130621
hg19 ljb2_siphy same as above 20130621
hg18 ljb23_siphy whole-exome SiPhy scores 20140222
hg19 ljb23_siphy same as above 20140222
hg18 ljb26_siphy whole-exome SiPhy scores 20140925
hg19 ljb26_siphy same as above 20140925
hg18 ljb_gerp++ whole-exome GERP++ scores 20120222
hg19 ljb_gerp++ same as above 20120222
hg18 ljb2_gerp++ whole-exome GERP++ scores 20130621
hg19 ljb2_gerp++ same as above 20130621
hg18 ljb23_gerp++ whole-exome GERP++ scores 20140222
hg19 ljb23_gerp++ same as above 20140222
hg18 ljb26_gerp++ whole-exome GERP++ scores 20140925
hg19 ljb26_gerp++ same as above 20140925
hg18 ljb23_metasvm whole-exome MetaSVM scores 20140222
hg19 ljb23_metasvm same as above 20140222
hg18 ljb26_metasvm whole-exome MetaSVM scores 20140925
hg19 ljb26_metasvm same as above 20140925
hg18 ljb23_metalr whole-exome MetaLR scores 20140222
hg19 ljb23_metalr same as above 20140222
hg18 ljb26_metalr whole-exome MetaLR scores 20140925
hg19 ljb26_metalr same as above 20140925
hg18 ljb26_vest whole-exome VEST scores 20140925
hg19 ljb26_vest same as above 20140925
hg18 ljb26_cadd whole-exome CADD scores 20140925
hg19 ljb26_cadd same as above 20140925
hg18 ljb_all whole-exome LJBSIFT, PolyPhen, PhyloP, LRT, MutationTaster, GERP++ scores 20120222
hg19 ljb_all same as above 20120222
hg18 ljb2_all whole-exome SIFT scores, PolyPhen2 HDIV scores, PolyPhen2 HVAR scores, LRT scores, MutationTaster scores, MutationAssessor score, FATHMM scores, GERP++ scores, PhyloP scores and SiPhy scores 20130621
hg19 ljb2_all same as above 20130621
hg18 ljb23_all whole-exome SIFT scores, PolyPhen2 HDIV scores, PolyPhen2 HVAR scores, LRT scores, MutationTaster scores, MutationAssessor score, FATHMM scores, MetaSVM scores, MetaLR scores, GERP++ scores, PhyloP scores and SiPhy scores 20140222
hg19 ljb23_all same as above 20140222
hg18 ljb26_all whole-exome SIFT scores, PolyPhen2 HDIV scores, PolyPhen2 HVAR scores, LRT scores, MutationTaster scores, MutationAssessor score, FATHMM scores, MetaSVM scores, MetaLR scores, VEST scores, CADD scores, GERP++ scores, PhyloP scores and SiPhy scores from dbsnp version 2.6 20140925
hg19 ljb26_all same as above 20140925
hg18 cg46 alternative allele frequency in 46 unrelated human subjects sequenced by Complete Genomics 20120222
hg19 cg46 same as above index updated 2012Feb22
hg18 cg69 allele frequency in 69 human subjects sequenced by Complete Genomics 20120222
hg19 cg69 same as above 20120222
hg19 cosmic64 COSMIC database version 64 20130520
hg19 cosmic65 COSMIC database version 65 20130706
hg19 cosmic67 COSMIC database version 67 20131117
hg19 cosmic67wgs COSMIC database version 67 on WGS data 20131117
hg19 cosmic68 COSMIC database version 68 20140224
hg19 cosmic68wgs COSMIC database version 68 on WGS data 20140224
hg19 cosmic70 same as above 20140911
hg18 esp5400_aa alternative allele frequency in African Americans in the NHLBI-ESP project with 5400 exomes 20120711
hg19 esp5400_aa same as above 20120711
hg18 esp5400_ea alternative allele frequency in European Americans in the NHLBI-ESP project with 5400 exomes 20120711
hg19 esp5400_ea same as above 20120711
hg18 esp5400_all alternative allele frequency in all subjects in the NHLBI-ESP project with 5400 exomes 20120711
hg19 esp5400_all same as above 20120711
hg18 esp6500_aa alternative allele frequency in African Americans in the NHLBI-ESP project with 6500 exomes 20120621
hg19 esp6500_aa same as above 20120621
hg18 esp6500_ea alternative allele frequency in European Americans in the NHLBI-ESP project with 6500 exomes 20120621
hg19 esp6500_ea same as above 20120621
hg18 esp6500_all alternative allele frequency in all subjects in the NHLBI-ESP project with 6500 exomes 20120621
hg19 esp6500_all same as above 20120621
hg18 esp6500si_aa alternative allele frequency in African Americans in the NHLBI-ESP project with 6500 exomes, including the indel calls and the chrY calls 20130122
hg19 esp6500si_aa same as above 20130122
hg18 esp6500si_ea alternative allele frequency in European Americans in the NHLBI-ESP project with 6500 exomes, including the indel calls and the chrY calls 20130122
hg19 esp6500si_ea same as above 20130122
hg18 esp6500si_all alternative allele frequency in all subjects in the NHLBI-ESP project with 6500 exomes, including the indel calls and the chrY calls 20130122
hg19 esp6500si_all same as above 20130122
hg18 esp6500siv2_ea alternative allele frequency in European American subjects in the NHLBI-ESP project with 6500 exomes, including the indel calls and the chrY calls. This is lifted over from hg19 by myself 20141222
hg19 esp6500siv2_ea same as above 20141222
hg38 esp6500siv2_ea same as above, lifted over from hg19 by myself 20141222
hg18 esp6500siv2_aa alternative allele frequency in African American subjects in the NHLBI-ESP project with 6500 exomes, including the indel calls and the chrY calls. This is lifted over from hg19 by myself. 20141222
hg19 esp6500siv2_aa same as above 20141222
hg38 esp6500siv2_aa same as above, lifted over from hg19 by myself 20141222
hg18 esp6500siv2_all alternative allele frequency in All subjects in the NHLBI-ESP project with 6500 exomes, including the indel calls and the chrY calls. This is lifted over from hg19 by myself. 20141222
hg19 esp6500siv2_all same as above 20141222
hg38 esp6500siv2_all same as above, lifted over from hg19 by myself 20141222
hg19 exac01 ExAC 65000 exome allele frequency data for ALL, AFR (African), AMR (Admixed American), EAS (East Asian), FIN (Finnish), NFE (Non-finnish European), OTH (other), SAS (South Asian)). 20141101
hg19 exac02 same as above but for version v0.2 20141101
hg19 exac03 same as above but for version 0.3 20150302
hg18 1000g (3 data sets) alternative allele frequency data in 1000 Genomes Project 20120222
hg18 1000g2010 (3 data sets) same as above 20120222
hg18 1000g2010jul (3 data sets) same as above 20120222
hg18 1000g2012apr I lifted over the latest 1000 Genomes Project data to hg18, to help researchers working with hg18 coordinates 20120820
hg19 1000g2010nov same as above 20120222
hg19 1000g2011may same as above 20120222
hg19 1000g2012feb same as above 20130308
hg18 1000g2012apr (5 data sets) This is done by liftOver of the hg19 data below. It contains alternative allele frequency data in 1000 Genomes Project for ALL, AMR (admixed american), EUR (european), ASN (asian), AFR (african) populations 20130508
hg19 1000g2012apr (5 data sets) alternative allele frequency data in 1000 Genomes Project for ALL, AMR (admixed american), EUR (european), ASN (asian), AFR (african) populations 20120525
hg19 1000g2014aug (6 data sets) alternative allele frequency data in 1000 Genomes Project for autosomes (ALL, AFR (African), AMR (Admixed American), EAS (East Asian), EUR (European), SAS (South Asian)). Based on 201408 collection v4 (based on 201305 alignment) 20140915
hg19 1000g2014sep (6 data sets) alternative allele frequency data in 1000 Genomes Project for autosomes (ALL, AFR (African), AMR (Admixed American), EAS (East Asian), EUR (European), SAS (South Asian)). Based on 201409 collection v5 (based on 201305 alignment) 20140925
hg19 1000g2014oct (6 data sets) alternative allele frequency data in 1000 Genomes Project for autosomes (ALL, AFR (African), AMR (Admixed American), EAS (East Asian), EUR (European), SAS (South Asian)). Based on 201409 collection v5 (based on 201305 alignment) but including chrX and chrY data finally! 20141216
hg18 snp128 dbSNP with ANNOVAR index files 20120222
hg18 snp129 same as above 20120222
hg19 snp129 liftover from hg18_snp129.txt 20120809
hg18 snp130 same as above 20120222
hg19 snp130 same as above 20120222
hg18 snp131 same as above 20120222
hg19 snp131 same as above 20120222
hg18 snp132 same as above 20120222
hg19 snp132 same as above 20120222
hg18 snp135 I lifted over SNP135 to hg18 20120820
hg19 snp135 same as above 20120222
hg19 snp137 same as above 20130109
hg18 snp138 I lifted over SNP138 to hg18 20140910
hg19 snp138 same as above file and index updated 20140910
hg18 snp128NonFlagged dbSNP with ANNOVAR index files, after removing those flagged SNPs (SNPs < 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated") 20120524
hg18 snp129NonFlagged same as above 20120524
hg18 snp130NonFlagged same as above 20120524
hg19 snp130NonFlagged same as above 20120524
hg18 snp131NonFlagged same as above 20120524
hg19 snp131NonFlagged same as above 20120524
hg18 snp132NonFlagged same as above 20120524
hg19 snp132NonFlagged same as above 20120524
hg19 snp135NonFlagged same as above 20120524
hg19 snp137NonFlagged same as above 20130109
hg19 snp138NonFlagged same as above 20140222
hg19 nci60 NCI-60 human tumor cell line panel exome sequencing allele frequency data 20130724
hg19 clinvar_20131105 CLINVAR database with Variant Clinical Significance (unknown, untested, non-pathogenic, probable-non-pathogenic, probable-pathogenic, pathogenic, drug-response, histocompatibility, other) and Variant disease name 20140430
hg19 clinvar_20140211 same as above 20140430
hg19 clinvar_20140303 same as above 20140430
hg19 clinvar_20140702 same as above 20140712
hg38 clinvar_20140702 same as above 20140712
hg19 clinvar_20140902 same as above 20140911
hg38 clinvar_20140902 same as above 20140911
hg19 clinvar_20140929 same as above 20141002
hg18 popfreq_max A database containing the maximum allele frequency from these tables: 1000G2012APR_ALL 1000G2012APR_AFR 1000G2012APR_AMR 1000G2012APR_ASN 1000G2012APR_EUR ESP6500si_ALL ESP6500si_AA ESP6500si_EA CG46 20130821
hg19 popfreq_max same as above 20130821
hg18 popfreq_all A database containing the all allele frequency from these tables: popfreq_max, 1000G2012APR_ALL 1000G2012APR_AFR 1000G2012APR_AMR 1000G2012APR_ASN 1000G2012APR_EUR ESP6500si_ALL ESP6500si_AA ESP6500si_EA CG46 20140223
hg19 popfreq_all same as above 20140223
hg18 gerp++elem conserved genomic regions by GERP++ 20140223
hg19 gerp++elem same as above 20140223
mm9 gerp++elem same as above 20140223
hg18 gerp++gt2 whole-genome GERP++ scores greater than 2 (RS score threshold of 2 provides high sensitivity while still strongly enriching for truly constrained sites. ) 20120621
hg19 gerp++gt2 same as above 20120621
hg19 caddgt20 whole-genome CADD scores that are within top 1% percentile, for most likely functional variants 20140310
hg19 caddgt10 whole-genome CADD scores that are within top 10% percentile, for most likely functional variants 20140310
hg19 cadd whole-genome CADD scores (350GB file, make sure you have sufficient disk space before downloading) 20140223
hg19 caddindel whole-genome CADDindel scores 20150325