SeqArray (version 1.12.5)

seqVCF_Header: Parse the Header of a VCF File

Description

Parses the header of a VCF file.

Usage

seqVCF_Header(vcf.fn, getnum=FALSE)

Arguments

vcf.fn

the file name; or a connection object

getnum

if TRUE, return the number of samples and variants

Value

Return a list (with a class name "SeqVCFHeaderClass", S3 object):

fileformat

the file format

info

the ID description in the INFO field

filter

the ID description in the FILTER field

format

the ID description in the FORMAT field

alt

the ID description in the ALT field

contig

the description in the contig field

assembly

the link of assembly

reference

genome reference, or NULL if unknown

header

the other header lines

ploidy

ploidy, two for humans

num.sample

the number of samples

num.variant

the number of variants

Details

The ID description contains four columns: ID -- variable name; Number -- the number of elements, see the webpage of the 1000 Genomes Project; Type -- data type; Description -- a variable description.

References

Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., et al. (2011). The variant call format and VCFtools. Bioinformatics 27, 2156-2158.

See Also

seqVCF_SampID, seqVCF2GDS

Examples

# the VCF file
(vcf.fn <- seqExampleFileName("vcf"))
# or vcf.fn <- "C:/YourFolder/Your_VCF_File.vcf"

# get sample id
seqVCF_Header(vcf.fn, getnum=TRUE)

# use a connection object
f <- file(vcf.fn, "r")
seqVCF_Header(f, getnum=TRUE)
close(f)