requires the vcfR package.
parse_pangolin(vcf_file)path to a single VCF file, the output of pangolin
a tibble with one row per variant annotation. Each input variant can have multiple annotations.
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>