requires the vcfR package.
parse_spliceai(vcf_file)path to a single VCF file, the output of spliceAI
a tibble with one row per variant annotation. Each input variant can have multiple annotations.
spliceai_file <- system.file("extdata", "spliceai_output.vcf", package = "splice2neo")
parse_spliceai(spliceai_file)
#> # A tibble: 15 × 18
#> CHROM POS ID REF ALT QUAL FILTER Key ALLELE SYMBOL DS_AG DS_AL
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <int> <chr> <chr> <dbl> <dbl>
#> 1 chr1 25000 NA A C,G,T NA NA 1 NA NA NA NA
#> 2 chr2 1523899… NA T A,C,G NA NA 2 A NEB 0.01 0
#> 3 chr2 1523899… NA T A,C,G NA NA 2 C NEB 0.04 0
#> 4 chr2 1523899… NA T A,C,G NA NA 2 G NEB 0.03 0
#> 5 chr2 1794159… NA C CA NA NA 3 CA TTN 0.07 1
#> 6 chr2 1794462… NA ATACT A NA NA 4 A TTN 0 0
#> 7 chr2 1794462… NA ATACT AT,A… NA NA 5 AT TTN NA NA
#> 8 chr2 1794462… NA ATACT AT,A… NA NA 5 ATA TTN NA NA
#> 9 chr2 1796421… NA G A NA NA 6 A TTN 0 0
#> 10 chr19 38958362 NA C T NA NA 7 T RYR1 0 0
#> 11 chr21 47406854 NA CCA C NA NA 8 C COL6A1 0.04 0.98
#> 12 chr21 47406856 NA A AT NA NA 9 AT COL6A1 0.03 0.99
#> 13 chrX 1292746… NA A C,G,T NA NA 10 C AIFM1 0 0.18
#> 14 chrX 1292746… NA A C,G,T NA NA 10 G AIFM1 0 0.17
#> 15 chrX 1292746… NA A C,G,T NA NA 10 T AIFM1 0 0.19
#> # ℹ 6 more variables: DS_DG <dbl>, DS_DL <dbl>, DP_AG <int>, DP_AL <int>,
#> # DP_DG <int>, DP_DL <int>