seqVCF_Header: Parse the Header of a VCF/BCF File

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

Description

Parses the meta-information lines of a VCF or BCF file.

Usage

seqVCF_Header(vcf.fn, getnum=FALSE)

Arguments

vcf.fn	the file name of VCF or BCF format; or a connection object for VCF format
getnum	if TRUE, return the total 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.

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, applicable only if getnum=TRUE
sample.id	a vector of sample IDs in the VCF/BCF file

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_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)

Example output

Loading required package: gdsfmt
[1] "/usr/lib/R/site-library/SeqArray/extdata/CEU_Exon.vcf.gz"
List of 13
 $ fileformat : chr "VCFv4.0"
 $ info       :'data.frame':	9 obs. of  6 variables:
  ..$ ID         : chr [1:9] "AA" "AC" "AN" "DP" ...
  ..$ Number     : chr [1:9] "." "1" "1" "1" ...
  ..$ Type       : chr [1:9] "String" "Integer" "Integer" "Integer" ...
  ..$ Description: chr [1:9] "Ancestral Allele" "Total number of alternate alleles in called genotypes" "Total number of alleles in called genotypes" "Total Depth" ...
  ..$ Source     : chr [1:9] NA NA NA NA ...
  ..$ Version    : chr [1:9] NA NA NA NA ...
 $ filter     :'data.frame':	2 obs. of  2 variables:
  ..$ ID         : chr [1:2] "PASS" "q10"
  ..$ Description: chr [1:2] "All filters passed" "Quality below 10"
 $ format     :'data.frame':	2 obs. of  4 variables:
  ..$ ID         : chr [1:2] "GT" "DP"
  ..$ Number     : chr [1:2] "1" "."
  ..$ Type       : chr [1:2] "String" "Integer"
  ..$ Description: chr [1:2] "Genotype" "Read Depth from MOSAIK BAM"
 $ alt        : NULL
 $ contig     : NULL
 $ assembly   : NULL
 $ reference  : chr "human_b36_both.fasta"
 $ header     :'data.frame':	0 obs. of  2 variables:
  ..$ id   : chr(0) 
  ..$ value: chr(0) 
 $ ploidy     : int 2
 $ num.sample : int 90
 $ num.variant: num 1348
 $ sample.id  : chr [1:90] "NA06984" "NA06985" "NA06986" "NA06989" ...
 - attr(*, "class")= chr "SeqVCFHeaderClass"
List of 13
 $ fileformat : chr "VCFv4.0"
 $ info       :'data.frame':	9 obs. of  6 variables:
  ..$ ID         : chr [1:9] "AA" "AC" "AN" "DP" ...
  ..$ Number     : chr [1:9] "." "1" "1" "1" ...
  ..$ Type       : chr [1:9] "String" "Integer" "Integer" "Integer" ...
  ..$ Description: chr [1:9] "Ancestral Allele" "Total number of alternate alleles in called genotypes" "Total number of alleles in called genotypes" "Total Depth" ...
  ..$ Source     : chr [1:9] NA NA NA NA ...
  ..$ Version    : chr [1:9] NA NA NA NA ...
 $ filter     :'data.frame':	2 obs. of  2 variables:
  ..$ ID         : chr [1:2] "PASS" "q10"
  ..$ Description: chr [1:2] "All filters passed" "Quality below 10"
 $ format     :'data.frame':	2 obs. of  4 variables:
  ..$ ID         : chr [1:2] "GT" "DP"
  ..$ Number     : chr [1:2] "1" "."
  ..$ Type       : chr [1:2] "String" "Integer"
  ..$ Description: chr [1:2] "Genotype" "Read Depth from MOSAIK BAM"
 $ alt        : NULL
 $ contig     : NULL
 $ assembly   : NULL
 $ reference  : chr "human_b36_both.fasta"
 $ header     :'data.frame':	0 obs. of  2 variables:
  ..$ id   : chr(0) 
  ..$ value: chr(0) 
 $ ploidy     : int NA
 $ num.sample : int 90
 $ num.variant: int 0
 $ sample.id  : chr [1:90] "NA06984" "NA06985" "NA06986" "NA06989" ...
 - attr(*, "class")= chr "SeqVCFHeaderClass"

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