annotation              Annotation function (single name)
annotation.cols.match   A position annotation utils that can be used to
                        write a yourself annotation function
annotation.merge        Annotation function (mulitple name)
annotation.region.match
                        A regeion annotation utils that can be used to
                        write a yourself annotation function
annovar                 R function to run ANNOVAR.
annovarR                The 'annovarR' package provides R functions as
                        well as database resources which offer an
                        integrated framework to annotate genetic
                        variants from genome and transcriptome data.
                        The wrapper functions of 'annovarR' unified the
                        interface of many published annotation tools,
                        such as 'VEP' (<URL:
                        http://asia.ensembl.org/info/docs/tools/vep/index.html>),
                        'ANNOVAR' (<URL:
                        http://annovar.openbioinformatics.org/>),
                        'vcfanno' (<URL:
                        https://github.com/brentp/vcfanno>) and
                        'AnnotationDbi' (<URL:
                        http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html>).
                        It also simplified the use of some of the
                        external annotation tools in R.  Besides,
                        massive published genetic variants annotation
                        databases were integrated into 'annovarR'.  For
                        example, 'annovarR' provides a newly RNA-seq
                        allele frequency database, BRVar, which built
                        from total 1,285 cases public B-progenitor
                        acute lymphoblastic leukemia (B-ALL)
                        transcriptome data.
del                     Delete table or database (text file, sqlite,
                        mysql)
download.database       Download annovarR databases
drop.mysql.index        Drop search index of annovarR database table in
                        mysql
drop.sqlite.index       Drop search index of annovarR database table in
                        sqlite
get.annotation.dbtype   Get annovarR default databases type [sqlite,
                        txt]
get.annotation.names    Get all annovarR supported databases
get.annotation.needcols
                        Get annovarR annotation needed colnames
                        according the anno.name
get.download.name       Use annotation name to get download.name that
                        can be used to download the database use
                        'download.database'
mysql.auto.build        Build annovarR database in mysql (auto from
                        extdata/config/database.toml)
mysql.auto.index        Index annovarR database in mysql (auto from
                        extdata/config/database.toml)
mysql.build             Build annovarR database in mysql
mysql.head              Show top n line of table of database in mysql
                        database
mysql.index             Generate search index of annovarR database
                        table in mysql
mysql.tb.colnames       Get colnames of table of database in mysql
mysql.tb.indexes        Get mysql table indexes
sql2sqlite              Convert sql file to sqlite database
sqlite.auto.build       Build annovarR database in sqlite (auto from
                        extdata/config/database.toml)
sqlite.auto.index       Index annovarR database in sqlite (auto from
                        extdata/config/database.toml)
sqlite.build            Build annovarR database in sqlite
sqlite.head             Show top n line of table of database in sqlite
                        database
sqlite.index            Generate search index of annovarR database
                        table in sqlite
sqlite.tb.colnames      Get colnames of table of database in sqlite
sqlite.tb.indexes       Get sqlite table indexes
sqlite2sql              Function to dump sqlite database (Now only use
                        system version sqlite)
vcfanno                 R function to run vcfanno
vep                     R function to run VEP
