Convert vcf info field to table format

Convert vcf info field to table format. Requires valid vcf where INFO fields are specified in header.

vcfInfo2Table(vcf, output, splitMultiallelic = TRUE)

Arguments

vcf

vcf file path.

output

output path

splitMultiallelic

Returns one row per alternative allele instead of one row per variant. Default=TRUE.

Examples

library(rvatData)
vcf <- rvat_example("rvatData.vcf.gz")
output <- tempfile()
vcfInfo2Table(
  vcf = vcf,
  output = output
)
#> Detected INFO field AC 
#> Detected INFO field AN 
#> Detected INFO field AF 
#> Detected INFO field gene_name 
#> Detected INFO field HighImpact 
#> Detected INFO field ModerateImpact 
#> Detected INFO field Synonymous 
#> Detected INFO field CADDphred 
#> Detected INFO field PolyPhen 
#> Detected INFO field SIFT