SeqArray (version 1.10.1)

seqVCF.Header: Parse the Header of a VCF File

Description

Parses the header of a VCF file.

Usage

seqVCF.Header(vcf.fn)

Arguments

vcf.fn

the file name of VCF

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

header

the other header lines

num.ploidy

the number of ploidy, two for humans

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

The variant call format and VCFtools. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group. Bioinformatics. 2011 Aug 1;27(15):2156-8. Epub 2011 Jun 7.

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)