Parse VCF output file from pangolin as table

Source: R/parse_pangolin.R

requires the vcfR package.

parse_pangolin(vcf_file)

Arguments

vcf_file

path to a single VCF file, the output of pangolin

Value

a tibble with one row per variant annotation. Each input variant can have multiple annotations.

Examples


pangolin_file <- system.file("extdata", "spliceai_output.pangolin.vcf", package = "splice2neo")
parse_pangolin(pangolin_file)
#> # A tibble: 25 × 11
#>    CHROM POS       ID    REF   ALT   QUAL  FILTER   Key gene_id          pos_rel
#>    <chr> <chr>     <chr> <chr> <chr> <chr> <chr>  <int> <chr>              <int>
#>  1 chr1  25000     NA    A     C,G,T NA    NA         1 ENSG00000227232…       8
#>  2 chr1  25000     NA    A     C,G,T NA    NA         1 ENSG00000227232…     -50
#>  3 chr2  152389953 NA    T     A,C,G NA    NA         2 ENSG00000183091…       2
#>  4 chr2  152389953 NA    T     A,C,G NA    NA         2 ENSG00000183091…       3
#>  5 chr2  179415988 NA    C     CA    NA    NA         3 ENSG00000237298…      33
#>  6 chr2  179415988 NA    C     CA    NA    NA         3 ENSG00000237298…     -50
#>  7 chr2  179415988 NA    C     CA    NA    NA         3 ENSG00000155657…     -26
#>  8 chr2  179415988 NA    C     CA    NA    NA         3 ENSG00000155657…      -1
#>  9 chr2  179446218 NA    ATACT A     NA    NA         4 ENSG00000237298…      14
#> 10 chr2  179446218 NA    ATACT A     NA    NA         4 ENSG00000237298…     -50
#> # ℹ 15 more rows
#> # ℹ 1 more variable: pangolin_score <dbl>