Parse VCF output file from SpliceAI with -T flag as table

requires the vcfR package.

parse_spliceai_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

parse_spliceai, format_spliceai_thresh, annotate_mut_effect

Examples

spliceai_file <- system.file("extdata", "spliceai_thresh_output.vcf", package = "splice2neo")
parse_spliceai_thresh(spliceai_file)
#> # A tibble: 22 × 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      NEB    AG      0.03
#>  3 chr2  152389… NA    T     A,C,G NA    NA         2 C      NEB    AL      0.5 
#>  4 chr2  179415… NA    C     CA    NA    NA         3 CA     TTN    AG      0.03
#>  5 chr2  179415… NA    C     CA    NA    NA         3 CA     TTN    AL      0.8 
#>  6 chr2  179415… NA    C     CA    NA    NA         3 CA     TTN    DG      0.08
#>  7 chr2  179415… NA    C     CA    NA    NA         3 CA     TTN    DL      0.5 
#>  8 chr2  179446… NA    ATACT A     NA    NA         4 A      TTN    AG      0.03
#>  9 chr2  179446… NA    ATACT A     NA    NA         4 A      TTN    DG      0.02
#> 10 chr2  179446… NA    ATACT AT,A… NA    NA         5 AT     TTN    AG      0.03
#> # ℹ 12 more rows
#> # ℹ 1 more variable: pos_rel <int>