Reads the virusbreakend.vcf file and selects data to present.
Value
List with two elements:
tab: Tibble containing selected data.descr: Description of tibble columns.
Examples
x <- system.file("extdata/virusbreakend/virusbreakend.vcf", package = "gpgr")
(vb <- virusbreakend_vcf_read(x))
#> $tab
#> # A tibble: 8 × 10
#> Contig Position `Fragment support` Fragment support (un…¹
#> <chr> <int> <dbl> <dbl>
#> 1 chr2 9728572 NA NA
#> 2 chr2 9942933 NA NA
#> 3 chr11 70486014 NA NA
#> 4 chr11 70488279 NA NA
#> 5 adjusted_kraken_taxid_3337… 1131 191 154
#> 6 adjusted_kraken_taxid_3337… 3351 37 27
#> 7 adjusted_kraken_taxid_3337… 4743 176 161
#> 8 adjusted_kraken_taxid_3337… 7066 32 28
#> # ℹ abbreviated name: ¹`Fragment support (unmapped)`
#> # ℹ 6 more variables: `Softclip read support` <dbl>, Reference <chr>,
#> # Alt <chr>, `Breakend ID` <chr>, `Mate ID` <chr>, QC <chr>
#>
#> $description
#> # A tibble: 10 × 2
#> Column Description
#> <chr> <chr>
#> 1 Contig Name of contig
#> 2 Position Position of breakend in contig
#> 3 Breakend ID ID of integration breakend
#> 4 Mate ID ID of integration breakend mate
#> 5 Reference Reference allele
#> 6 Alt Alternative allele
#> 7 QC VCF filter values
#> 8 Fragment support Total number of fragments supporting breakend
#> 9 Fragment support (unmapped) Number of fragments supporting breakend that hav…
#> 10 Softclip read support Number of softclipped reads supporting breakend
#>