Parse VCF output file from CI-SpliceAI with -t flag as table

requires the vcfR package.

parse_cispliceai_thresh(vcf_file)

Arguments

vcf_file

path to a single VCF file, the output of spliceAI

Value

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

See also

format_cispliceai_thresh, annotate_mut_effect

Examples

cispliceai_file <- system.file("extdata", "cispliceai_thresh_output.vcf", package = "splice2neo")
parse_cispliceai_thresh(cispliceai_file)
#> # A tibble: 23 × 13
#>    CHROM POS     ID    REF   ALT   QUAL  FILTER   Key ALLELE SYMBOL effect score
#>    <chr> <chr>   <chr> <chr> <chr> <chr> <chr>  <int> <chr>  <chr>  <fct>  <dbl>
#>  1 chr1  25000   NA    A     C,G,T NA    NA         1 NA     NA     NA     NA   
#>  2 chr2  152389… NA    T     A,C,G NA    NA         2 A      ENSG0… DL      0.96
#>  3 chr2  152389… NA    T     A,C,G NA    NA         2 C      ENSG0… DL      0.9 
#>  4 chr2  152389… NA    T     A,C,G NA    NA         2 G      ENSG0… DL      0.97
#>  5 chr2  179415… NA    C     CA    NA    NA         3 CA     ENSG0… AL      1   
#>  6 chr2  179415… NA    C     CA    NA    NA         3 CA     ENSG0… AG      0.05
#>  7 chr2  179415… NA    C     CA    NA    NA         3 CA     ENSG0… AG      0.03
#>  8 chr2  179415… NA    C     CA    NA    NA         3 CA     ENSG0… AG      0.04
#>  9 chr2  179446… NA    ATACT A     NA    NA         4 A      ENSG0… DG      0.03
#> 10 chr2  179446… NA    ATACT A     NA    NA         4 A      ENSG0… DL      0.87
#> # ℹ 13 more rows
#> # ℹ 1 more variable: pos_rel <int>