vcf2annovar: vcf2annovar

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

Description

A wrapper function to run vcf2annovar.pl in ANNOVAR

Usage

vcf2annovar(fns.vcf, output.dir, sample.name, format="vcf4", coverage=0, run.cmd=TRUE, mc.cores=1)

Arguments

fns.vcf	Path to VCF files
output.dir	Output directory
sample.name	A character vector for the sample names
format	A parameter value for -format in ANNOVAR Input files format (.vcf)
coverage	A parameter value for -coverage in ANNOVAR Read coverage threshold in pileup file (default:0)
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

The convert2annovar.pl script convert other "genotype calling" format into ANNOVAR format. Additionally, the program can generate ANNOVAR input files from a list of dbSNP identifiers, or from transcript identifiers, or from a genomic region.

Value

Converted annovar files from variant calling format (e.g., .annovar)

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.