read.vcf: Read VCF file

Description Usage Arguments Value Author(s) See Also Examples

View source: R/readvcf.R

Description

Load VCF format file of variant and/or sequence calls into a flexible VCF object in R environment.

Usage

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read.vcf(file, VCF=NULL, INFOID = NULL, FORMATID = NULL, ...)

Arguments

file

VCF format file of sequence calls from tools such as samtools and GATK.

VCF

An object list from the function pos2seq output.

INFOID

Characters. Only specified elements in INFO column of VCF file will be read.

FORMATID

Characters. Only specified elements in FORMAT column of VCF file will be read.

...

not used.

Value

A vcf object. Also it is a list. Each element of the list is from a column of the VCF file. See HEAD for details.

Author(s)

Qiang Hu

See Also

write.vcf

Examples

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##read example vcf file in data directory.
vcffile <- system.file("extdata", "1151HZ0001.flt.vcf", package="VPA")
vcfdata <- read.vcf(vcffile)
summary(vcfdata)
write.vcf(vcfdata)

VPA documentation built on May 2, 2019, 4:45 p.m.