Utilities for VCF format

as_vcf() converts a SNP data.frame generated by make_snp() to a VCF-like data.frame. Only the "CHROM", "FORMAT", and "gt" columns are filled.

add_pos_id() is useful to fill the "POS" and "ID" columns. it assigns sequential integers to the "POS" column for each "CHROM", and combines it with "CHROM" to make a unique "ID" values.

write_vcf() and read_vcf() are used to write and read VCF files. If a SNP data.frame is given, it is converted before writing.

Usage

as_vcf(x, phased = TRUE, chrom = NA_character_, pos = NA_integer_)

add_pos_id(x)

write_vcf(x, file)

read_vcf(file)

as_vcf_gt(x, phased = TRUE)

Arguments

x

A SNP data.frame or VCF data.frame.

phased

A logical to switch separators: | vs /.

chrom

Characters.

pos

Integers.

file

A path or connection.

Value

A VCF-like data.frame with "vcf" subclass.

as_vcf_gt() returns a single-column data.frame with "vcf_gt" subclass.

See also

make_snp() to generate SNP data.frames.

https://samtools.github.io/hts-specs/ for VCF format specification.

Examples

RNGkind("L'Ecuyer-CMRG")
set.seed(666)
result = tekka("-y20 -l2 --sa 2,2 --sj 2,2")
samples = result$sample_family[[1L]]
ss = c(chr1 = 3, chr2 = 2)
snp = make_snp(samples, ss)
vcf = as_vcf(snp) |> add_pos_id()
vcf
#> # A tibble: 5 × 10
#>   CHROM   POS ID     REF   ALT   QUAL  FILTER INFO  FORMAT gt                   
#>   <chr> <int> <chr>  <chr> <chr> <chr> <chr>  <chr> <chr>  <chr>                
#> 1 chr1      1 chr1-1 NA    NA    NA    NA     NA    GT     "0|0\t0|0\t0|0\t0|0\…
#> 2 chr1      2 chr1-2 NA    NA    NA    NA     NA    GT     "0|0\t0|0\t0|0\t0|0\…
#> 3 chr1      3 chr1-3 NA    NA    NA    NA     NA    GT     "0|1\t0|0\t0|0\t0|0\…
#> 4 chr2      1 chr2-1 NA    NA    NA    NA     NA    GT     "0|0\t0|0\t0|0\t0|0\…
#> 5 chr2      2 chr2-2 NA    NA    NA    NA     NA    GT     "0|0\t0|0\t0|0\t0|0\…