vcf.to.sigs.input breaks when file contains annotations (ID field)

[markozecevic]

Hi,

when processing VCF files with partially (or fully) annotated ID field using the readGT function, what you get back is a matrix looking like this:

> gt <- readGT(vcf, nucleotides = TRUE)
> head(gt)
               tumor
1:6610695_G/A  "G/A"
1:15654752_C/T "C/T"
1:16248740_A/T "A/T"
1:40928079_A/T "A/T"
rs2596251      "G/A"
rs75758917     "G/T"

Some row names are dbSNP IDs, which makes it impossible to obtain chromosome, position or reference information the way it is done in the vcf.to.sigs.input function.

    chr <- sub(":.+", "", rownames(gt))
    pos <- as.numeric(sub("_.+", "", sub(".+:", "", rownames(gt))))
    ref <- sub("[/|].+", "", sub(".+_", "", rownames(gt)))

Is there a reason other than readGT being lightweight, that a more general solution like this below is not used?

    auxVcf <- readVcf(vcf)
    chr <- as.character(seqnames(auxVcf))
    pos <- start(auxVcf)
    ref <- as.character(ref(auxVcf))

Thanks for all the work!

Marko