# NOT RUN {
# 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)
# }
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