table.annovar: table.annovar

In omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Description

A wrapper function to run table_annovar.pl in ANNOVAR

Usage

table.annovar(fn.annovar, output.dir, sample.name, annovar.db, ref="hg38", protocol="refGene,cytoBand,genomicSuperDups,esp6500siv2_all,1000g2015aug_all,exac03,avsnp147,ljb26_all,cosmic70", protocol.type="g,r,r,f,f,f,f,f,f", nastring=".", run.cmd=TRUE, mc.cores=1)

Arguments

fns.annovar	Path to annovar files
output.dir	Output directory
sample.name	A character vector for the sample names
annovar.db.dir	Path to directory with ANNOVAR database
ref	A parameter value for -buildver in ANNOVAR. Specify the genome build version (default: hg38)
protocol	A parameter value for -protocol in ANNOVAR Database names in ANNOVAR (default: "refGene,cytoBand,genomicSuperDups,esp6500siv2_all,1000g2015aug_all,exac03,avsnp147,ljb26_all,cosmic70")
protocol.type	A parameter value for -operation in ANNOVAR. Strings separated by commas that specify the types of operation for each protocol (g: genome, r: region, f: filter, default="g,r,r,f,f,f,f,f,f")
nastring	A parameter value for -nastring in ANNOVAR. Strings to display when a score is not available (default: ".")
run.cmd	Whether to execute the command line (default=TRUE)
mc.cores	The number of cores to use. Must be at least one(default=1), and parallelization requires at least two cores.

Details

This function takes an input variant file (such as a VCF file) and generate a tab-delimited output file with many columns, each representing one set of annotations. Additionally, if the input is a VCF file, the program also generates a new output VCF file with the INFO field filled with annotation information.

Value

CSV files from annovar format

References

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

See Also

http://annovar.openbioinformatics.org/en/latest/user-guide/

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.