extracting info field from VCF using vcfr

Question

[j.lunger18]

I used several tools to annotate a list of variants and now have a VCF file with a long info field. I'm trying to use the 'vcfr' package in R to start data analysis, but it seems to have a problem reading my info field, which is separated by semi-colons (edit; I previously said it was separated by colons). Here is what I did:

head(vcf_file) 
[1] "***** Object of class 'vcfR' *****"
[1] "***** Meta section *****"
[1] "##fileformat=VCFv4.2"
[1] "##hailversion=devel-784ab2796878"
[1] "##FILTER=<ID=AC0,Description=\"Allele count is zero after filtering o [Truncated]"
[1] "##FILTER=<ID=InbreedingCoeff,Description=\"InbreedingCoeff < -0.3\">"
[1] "##FILTER=<ID=PASS,Description=\"Passed all variant filters\">"
[1] "##FILTER=<ID=RF,Description=\"Failed random forest filtering threshol [Truncated]"
[1] "First 6 rows."
[1] 
[1] "***** Fixed section *****"
     CHROM POS         ID             REF   ALT QUAL      FILTER
[1,] "4"   "119606531" "rs1429579493" "A"   "G" "157.46"  "PASS"
[2,] "4"   "119606549" "rs998903473"  "GTC" "G" "609.46"  "PASS"
[3,] "4"   "119606551" "rs992734531"  "C"   "A" "1821.94" "PASS"
[4,] "4"   "119606553" "rs568037846"  "C"   "G" "8320.87" "PASS"
[5,] "4"   "119606555" "rs536993934"  "A"   "C" "2326.65" "PASS"
[6,] "4"   "119606556" NA             "C"   "T" "297.46"  "PASS"
[1] 
[1] "***** Genotype section *****"
<0 x 0 matrix>
[1] 
[1] "Unique GT formats:"
[1] "No gt slot present"

Seeing that it didn't give me a genotype section, I tried:

extract.gt(vcf_file)
Error in if (colnames(x@gt)[1] != "FORMAT") { : 
  argument is of length zero

I'm positive that there is a long INFO field because I opened this file up in excel and saw it...

[Brice Sarver]

Why not write an expression to sub out the colons in the INFO field and replace with semicolons?

Edit: the justification for this suggestion, from the VCF specification -

INFO - additional information: (String, no white-space, semi-colons, or equals-signs permitted; commas are permitted only as delimiters for lists of values) INFO fields are encoded as a semicolon-separated series of short keys with optional values in the format: <key>=<data>[,data]. Arbitrary keys are permitted, although the following sub-fields are reserved (albeit optional):

[j.lunger18]

My bad. I meant semicolons!