seqVCF_SampID: Get the Sample IDs

In SeqArray: Data management of large-scale whole-genome sequence variant calls

Description

Returns the sample IDs of a VCF file.

Usage

seqVCF_SampID(vcf.fn)

Arguments

vcf.fn

the file name, output a file of VCF format; or a connection object

Author(s)

Xiuwen Zheng

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_Header, seqVCF2GDS

Examples

# the VCF file
(vcf.fn <- seqExampleFileName("vcf"))

# get sample id
seqVCF_SampID(vcf.fn)

Example output

Loading required package: gdsfmt
[1] "/usr/lib/R/site-library/SeqArray/extdata/CEU_Exon.vcf.gz"
 [1] "NA06984" "NA06985" "NA06986" "NA06989" "NA06994" "NA07000" "NA07037"
 [8] "NA07048" "NA07051" "NA07346" "NA07347" "NA07357" "NA10847" "NA10851"
[15] "NA11829" "NA11830" "NA11831" "NA11832" "NA11840" "NA11843" "NA11881"
[22] "NA11893" "NA11918" "NA11919" "NA11920" "NA11930" "NA11992" "NA11994"
[29] "NA11995" "NA12003" "NA12004" "NA12005" "NA12006" "NA12043" "NA12044"
[36] "NA12045" "NA12058" "NA12144" "NA12154" "NA12155" "NA12156" "NA12234"
[43] "NA12249" "NA12272" "NA12273" "NA12275" "NA12282" "NA12283" "NA12286"
[50] "NA12287" "NA12340" "NA12341" "NA12342" "NA12347" "NA12348" "NA12383"
[57] "NA12400" "NA12413" "NA12414" "NA12489" "NA12546" "NA12716" "NA12717"
[64] "NA12718" "NA12748" "NA12749" "NA12750" "NA12751" "NA12760" "NA12761"
[71] "NA12762" "NA12763" "NA12775" "NA12776" "NA12812" "NA12814" "NA12815"
[78] "NA12828" "NA12829" "NA12830" "NA12842" "NA12843" "NA12872" "NA12873"
[85] "NA12874" "NA12878" "NA12889" "NA12890" "NA12891" "NA12892"

SeqArray documentation built on Nov. 8, 2020, 5:08 p.m.