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简介
Region-based annotation是基于区域进行注释的，它不用考虑精确位置也不考虑核苷酸的同一性。进行注释时要使用--regionanno 参数(默认是 --geneanno )，缩写
包含的数据库
- Conserved genomic elements annotation
- Transcription factor binding site
- Identify cytogenetic band
- Identify variants disrupting microRNAs and snoRNAs
- Identify variants disrupting predicted microRNA binding sites
- Identify variants located in segmental duplications
- Identify previously reported structural variants
- Identify variants reported in previously published GWAS
- Identify variants in ENCODE annotated regions
- Identify dbSNP variants in user-specified regions
- Identify non-coding variants that disrupt enhancers, repressors, promoters
- Identify variants in other genomic regions annotated with other functions
- Annotating custom-made databases conforming to GFF3 (Generic Feature Format version 3)
- Identifying variants in regions specified in BED files
Conserved genomic elements annotation 保守基因组注释
用来鉴定保守基因组区域的变体 。-dbtype phastConsElements46way
#下载
annotate_variation.pl -build hg19 -downdb phastConsElements46way humandb/
NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done
NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/phastConsElements46way.txt.gz ... OK
NOTICE: Uncompressing downloaded files
NOTICE: Finished downloading annotation files for hg19 build version, with files saved at the 'humandb' directory
#注释
annotate_variation.pl -regionanno -build hg19 -out ex1 -dbtype phastConsElements46way example/ex1.avinput humandb/
NOTICE: Reading annotation database humandb/hg19_phastConsElements46way.txt ... Done with 5163775 regions
结果说明
phastConsElements46way Score=420;Name=lod=68 16 50756540 50756540 G C comments: rs2066845 (G908R), a non-synonymous SNP in NOD2
phastConsElements46way Score=385;Name=lod=49 16 50763778 50763778 - C comments: rs2066847 (c.3016_3017insC), a frameshift SNP in NOD2
phastConsElements46way Score=395;Name=lod=54 13 20763686 20763686 G - comments: rs1801002 (del35G), a frameshift mutation in GJB2, associated with hearing loss
phastConsElements46way Score=545;Name=lod=218 13 20797176 21105944 0 - comments: a 342kb deletion encompassing GJB6, associated with hearing loss
第一列 phastConsElements46way：表示注释的类型；
第二列：表示分数和名称，分数是UCSC Genome Browser分配的归一化分数，该分数范围从0到1000，其目的是在浏览器中显示标准值范围；
他列与输入文件中的列完全相同。只有实际位于保守区域内的变体才会打印在输出文件中
Transcription factor binding site 转录因子结合位点
包含人/小鼠/大鼠比对中保守的转录因子结合位点的位置和分数，其中得分和阈值使用Transfac Matrix Database计算，-dbtype tfbsConsSites
#下载
annotate_variation.pl -build hg19 -downdb tfbsConsSites humandb/
#注释
annotate_variation.pl -regionanno -build hg19 -out ex1 -dbtype tfbsConsSites example/ex1.avinput humandb/
#结果文件
tfbsConsSites Score=767;Name=V$PAX5_02 16 50745926 50745926 C T comments: rs2066844 (R702W), a non-synonymous SNP in NOD2
tfbsConsSites Score=880;Name=V$CEBPA_01 16 50756540 50756540 G C comments: rs2066845 (G908R), a non-synonymous SNP in NOD2
tfbsConsSites Score=878;Name=V$FREAC3_01 13 20763686 20763686 G - comments: rs1801002 (del35G), a frameshift mutation in GJB2, associated with hearing loss
tfbsConsSites Score=1000;Name=V$STAT4_01,V$AML1_01,V$SRY_01,V$MZF1_01 13 20797176 21105944 0 - comments: a 342kb deletion encompassing GJB6, associated with hearing loss
第二列具有分数和名称注释，表示标准化分数和结合位点主题名称。诸如V $ PAX5_02之类的名称仅表示某些转录因子识别的主题的名称。由用户来决定哪些转录因子可以识别该基序。
Identify cytogenetic band 细胞遗传学带识别
为了鉴定Giemsa染色的染色体条带，可以使用-dbtype cytoBand
#下载
annotate_variation.pl -build hg19 -downdb cytoBand humandb/
#注释
annotate_variation.pl -regionanno -build hg19 -out ex1 -dbtype cytoBand example/ex1.avinput humandb/
#结果文件
cytoBand 1q23.3 1 162736463 162736463 C T comments: rs1000050, a SNP in Illumina SNP arrays
cytoBand 1p31.1 1 84875173 84875173 C T comments: rs6576700 or SNP_A-1780419, a SNP in Affymetrix SNP arrays
cytoBand 1p36.21 1 13211293 13211294 TC - comments: rs59770105, a 2-bp deletion
cytoBand 1p36.22 1 11403596 11403596 - AT comments: rs35561142, a 2-bp insertion
Identify variants disrupting microRNAs and snoRNAs 确定破坏microRNA和snoRNA的变体
UCSC基于miRBase Release和snoRNABase提供snoRNA和microRNA的wgRna表 。可以使用-dbtype wgRna
#下载
annotate_variation.pl -build hg19 -downdb wgRna humandb/
#注释
annotate_variation.pl -regionanno -build hg19 -out ex1 -dbtype wgRna example/ex1.avinput humandb/
Identify variants disrupting predicted microRNA binding sites 鉴定破坏预测的microRNA结合位点的变体。
发现破坏预测的microRNA结合位点的变体。 UCSC提供TargetScanS注释数据库，该数据库显示保守的哺乳动物microRNA调控靶位点，用于Refseq基因的3'UTR区域中保守的microRNA家族，可以使用-dbtype targetScanS
#下载
annotate_variation.pl -build hg19 -downdb targetScanS humandb/
#注释
annotate_variation.pl -regionanno -build hg19 -out ex1 -dbtype targetScanS example/ex1.avinput humandb/
Identify variants located in segmental duplications 识别位于分段重复中的变体
映射到节段重复的遗传变异很可能是序列比对错误，有时它们表现为具有高折叠覆盖率且可能具有高置信度得分的SNP，实际上可能代表基因组中恰好具有相同侧翼序列的两个非多态性位点。可以使用-dbtype genomicSuperDups
#下载
annotate_variation.pl -build hg19 -downdb genomicSuperDups humandb/
#注释
annotate_variation]$ annotate_variation.pl -regionanno -build hg19 -out ex1 -dbtype genomicSuperDups example/ex1.avinput humandb/
#结果文件
genomicSuperDups Score=0.99612;Name=chr1:13142561 1 13211293 13211294 TC - comments: rs59770105, a 2-bp deletion
输出中的“名称”字段表示基因组中的另一个“匹配”区段（其位于chr1：13142561处的相同染色体中）。 “得分”字段是两个基因组区段之间具有indel的序列同一性。
Identify previously reported structural variants 已报道的结构变异确定
ANNOVAR还可以方便地对缺失和重复进行注释，并将它们与基因组变体数据库（DGV）中先前发表的变体进行比较，--dbtype dgvMerged。
#下载
annotate_variation.pl -build hg19 -downdb dgvMerged humandb/
#注释
annotate_variation.pl -regionanno -build hg19 -out ex1 -dbtype dgvMerged example/ex1.avinput humandb/
#结果文件
dgvMerged Name=nsv516482 1 162736463 162736463 C T comments: rs1000050, a SNP in Illumina SNP arrays
dgvMerged Name=nsv830437 1 84875173 84875173 C T comments: rs6576700 or SNP_A-1780419, a SNP in Affymetrix SNP arrays
dgvMerged Name=dgv168n71,nsv821616,nsv510936,nsv871634,esv27872,nsv870885,dgv147n71,nsv517190,nsv821333,nsv871687,nsv7172,nsv428410,nsv8768,dgv20e1,dgv22e1 1 13211293 13211294 TC - comments: rs59770105, a 2-bp deletion
dgvMerged Name=nsv832536 1 11403596 11403596 - AT comments: rs35561142, a 2-bp insertion
对于删除和重复的结构变体，-minqueryoverlap可以去除SNP或indel重叠（否则许多SNP / indel将与DGV区域重叠）
Identify variants reported in previously published GWAS 确定在GWAS中已报道的变体
查找先前报告的与全基因组关联研究中的疾病或性状相关的变体，可以使用 -dbtype gwasCatalog
#下载
annotate_variation.pl -build hg19 -downdb gwasCatalog humandb/
#注释
annotate_variation.pl -regionanno -build hg19 -out ex1 -dbtype gwasCatalog example/ex1.avinput humandb/
#结果文件
gwasCatalog Name=Ankylosing spondylitis,Crohn's disease,Ulcerative colitis,Psoriasis,Inflammatory bowel disease 1 67705958 67705958 comments: rs11209026 (R381Q), a SNP in IL23R associated with Crohn's disease
gwasCatalog Name=Crohn's disease 2 234183368 234183368 A G comments: rs2241880 (T300A), a SNP in the ATG16L1 associated with Crohn's disease
gwasCatalog Name=Crohn's disease 16 50763778 50763778 - C comments: rs2066847 (c.3016_3017insC), a frameshift SNP in NOD2
Identify variants in ENCODE annotated regions识别ENCODE注释区域中的变体
ENCODE现在在ANNOVAR可以注释的基因组浏览器轨道中提供大量数据，例如转录区域，H3K4Me1区域，H3K4Me3区域，H3K27Ac区域，DNaseI超敏感区域，转录因子ChIP-Seq区域等。
Identify dbSNP variants in user-specified regions识别用户指定区域中的dbSNP变体
这与基于过滤的注释不同。在这里，我们只关心两个区域是否有重叠，而不是相同。因此，删除区域可以匹配dbSNP数据库中的多个SNP。-dbtype snp138
