Read VCF with SNVs/INDELs for use with HRDetect

Reads a VCF with SNVs/INDELs for use with HRDetect.

Usage

hrdetect_read_snvindel_vcf(x)

Arguments

x

Path to VCF.

Value

List containing CHROM, POS, REF and ALT columns for SNVs and INDELs in separate tibbles.

Examples

x <- system.file("extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz", package = "gpgr")
(l <- hrdetect_read_snvindel_vcf(x))
#> $snv
#> # A tibble: 5,944 × 4
#>    chr   position REF   ALT  
#>    <chr>    <int> <chr> <chr>
#>  1 chr1   1303273 C     T    
#>  2 chr1   4932638 C     G    
#>  3 chr1   5545493 T     A    
#>  4 chr1   6434166 G     T    
#>  5 chr1   6654913 C     G    
#>  6 chr1   6961437 C     G    
#>  7 chr1   7057562 A     T    
#>  8 chr1   7945201 A     T    
#>  9 chr1  10020499 A     C    
#> 10 chr1  10148616 G     A    
#> # ℹ 5,934 more rows
#> 
#> $indel
#> # A tibble: 765 × 4
#>    chr   position REF           ALT  
#>    <chr>    <int> <chr>         <chr>
#>  1 chr1   3003408 TGCAGAGA      T    
#>  2 chr1   3708171 AG            A    
#>  3 chr1   4177626 TC            T    
#>  4 chr1   8384452 AG            A    
#>  5 chr1  13261670 CT            C    
#>  6 chr1  16121339 AT            A    
#>  7 chr1  37142428 AG            A    
#>  8 chr1  52675033 GC            G    
#>  9 chr1  56208467 TC            T    
#> 10 chr1  56810765 CTTTAACAGAGAT C    
#> # ℹ 755 more rows
#>