Read a VCF file.
Note
return value has chrom, start and end columns.
Interval lengths are the size of the 'REF' field.
See also
Other read functions:
read_bed(),
read_genome()
Examples
vcf_file <- valr_example("test.vcf.gz")
read_vcf(vcf_file)
#> # A tibble: 11 × 18
#> CHROM POS ID REF ALT QUAL FILTER INFO FORMAT X1 X2
#> <chr> <dbl> <chr> <chr> <chr> <dbl> <chr> <chr> <chr> <chr> <chr>
#> 1 1 10 1:10 A T 100 PASS NS=5;A… GT 0/0 ./.
#> 2 1 20 1:20 G C 100 PASS NS=0;A… GT ./. ./.
#> 3 1 30 1:30 C A 100 PASS NS=6;A… GT 0/0 0/0
#> 4 1 40 1:40 A C 100 PASS NS=6;A… GT 0/0 0/0
#> 5 1 10000 1:10000 G C 100 PASS NS=6;A… GT 0/0 0/0
#> 6 1 20000 1:20000 T A 100 PASS NS=6;A… GT 1/1 1/1
#> 7 4 5000 4:5000 A T 100 PASS NS=6;A… GT 1/1 1/1
#> 8 4 6000 4:6000 C T 100 PASS NS=6;A… GT 1/1 1/1
#> 9 X 800 X:800 A C 100 PASS NS=6;A… GT 1/1 1/1
#> 10 X 900 X:900 A T 100 PASS NS=6;A… GT 1/1 1/1
#> 11 X 1000 X:1000 T G 100 PASS NS=5;A… GT 1/1 1/1
#> # ℹ 7 more variables: X3 <chr>, X4 <chr>, X5 <chr>, X6 <chr>,
#> # chrom <chr>, start <dbl>, end <dbl>