annovar: R function to run ANNOVAR.

In JhuangLab/annovarR: Integrated Framework to Annotate Genetic Variants

Description

R function to run ANNOVAR.

Usage

annovar(
  perl = Sys.which("perl"),
  cmd.pool = list(script1.downdb = paste(c("{perl}", "{script}{extra.params}",
    "-downdb", "{buildver}", "{webfrom}", "{down.dbname}", "{database.dir}"), collapse =
    " "), script1.gene.based = paste(c("{perl}", "{script}{extra.params}", "{buildver}",
    "{input.file}", "{database.dir}"), collapse = " "), script1.region.based =
    paste(c("{perl}", "{script}", " -regionanno{extra.params}", "{buildver}",
    "{anno.names}", "{input.file}", "{database.dir}"), collapse = " "),
    script1.filter.based = paste(c("{perl}", "{script}",      "-filter{extra.params}",
    "{buildver}", "{anno.names}", "{input.file}", "{database.dir}"), collapse = " "),
    script2 = paste(c("{perl}", "{script}", "{input.file}", "{database.dir}",
    "{buildver}", "{out}", "-remove{extra.params}", "-protocol {anno.names}",
    "-operation", "{operation}", "{nastring}", "{otherinfo}", "{vcfinput}"), collapse =
    " "), script3 = paste("{perl}", "{script}{extra.params}", "-format", "{format}",
    "{input.file}", "> {convert.out}", collapse = " ")),
  cmd_used = "script1.downdb",
  down.dbname = "",
  input.file = "",
  annovar.dir = "",
  buildver = "hg19",
  database.dir = "{annovar.dir}/humandb",
  webfrom = "annovar",
  anno.names = "",
  out = "",
  convert.out = "",
  format = "vcf4",
  operation.type = list(gene.based = c("refGene", "knownGene", "ensGene", "ccdsGene"),
    region.based = c("cytoBand", "genomicSuperDups")),
  cmd.profix.flag = list(buildver = "-buildver", anno.names = "-dbtype", webfrom =
    "-webfrom", out = "-out", nastring = "-nastring"),
  otherinfo = FALSE,
  nastring = "NA",
  vcfinput = FALSE,
  extra.params = "",
  debug = FALSE
)

Arguments

perl	Executable file of perl
cmd.pool	Un-parsed commands of ANNOVAR
cmd_used	Name in cmd.pool that used to parse final run command
down.dbname	Need to download database name, e.g. avsnp147,cosmic70,1000g2015aug
input.file	Input file name, e.g. example.avinput, example.vcf
annovar.dir	ANNOVAR source code directory
buildver	Genome version e.g. hg19, mm10
database.dir	Database directory, e.g. /opt/annovar/humandb
webfrom	Database resource warehouse, e.g. ucsc, annovar
anno.names	ANNOVAR annotation names
out	ANNOVAR -out parameter value
convert.out	ANNOVAR convert2annovar.pl output file, e.g. out.avinput
format	ANNOVAR convert2annovar.pl input format option
operation.type	Operation types used in table_annovar.pl
cmd.profix.flag	Profix used in ANNOVAR command
otherinfo	Used in table_annovar.pl, -otherinfo
nastring	ANNOVAR -nastring value, default is NA.
vcfinput	Specify that input is in VCF format and output will be in VCF format, table_annovar.pl, -vcfinput
extra.params	Extra paramters in ANNOVAR command
debug	If set TRUE, only print the command

Examples

# original ANNOVAR download.database
down.dbname <- 'refGene'
annovar('perl', cmd_used = 'script1.downdb', down.dbname = 'avsnp147',
        annovar.dir = '/opt/annovar', debug = TRUE)

# ANNOVAR gene-based annotation
annovar('perl', cmd_used = 'script1.gene.based', input.file = 'example.avinput',
        annovar.dir = '/opt/annovar', debug = TRUE)

# ANNOVAR gene-based annotation
annovar('perl', cmd_used = 'script1.region.based', anno.names = 'cytoBand',
        input.file = 'example.avinput', annovar.dir = '/opt/annovar', debug = TRUE)

# ANNOVAR filter-based annotation
annovar('perl', cmd_used = 'script1.filter.based', anno.names = 'avsnp147',
        input.file = 'example.avinput', annovar.dir = '/opt/annovar', debug = TRUE)

# ANNOVAR table_annovar.pl
anno.names <- c('refGene','cytoBand','genomicSuperDups','esp6500siv2_all',
'1000g2015aug_all','1000g2015aug_afr','1000g2015aug_eas','1000g2015aug_eur',
'snp138','avsnp142','avsnp144','avsnp147','ljb26_all','cosmic70','cosmic81')
annovar('perl', cmd_used = 'script2',
        anno.names = anno.names,
        input.file = 'example.avinput', annovar.dir = '/opt/annovar', debug = TRUE)

# ANNOVAR convert2annovar.pl
annovar('perl', cmd_used = 'script3', input.file = 'example.vcf', format = 'vcf4old',
        convert.out = 'example.avinput', annovar.dir = '/opt/annovar', debug = TRUE)

JhuangLab/annovarR documentation built on April 23, 2020, 10:51 p.m.