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Read VCF with SVs for use with HRDetect

Source: R/hrdetect.R
hrdetect_read_sv_vcf.Rd

Reads a VCF with SVs for use with HRDetect.

Usage

hrdetect_read_sv_vcf(x, nm = NULL, genome = "hg38")

Arguments

x

Path to VCF.

nm

Sample name.

genome

Human genome version (default: hg38. hg19 means GRCh37).

Value

Tibble with following BEDPE-like columns:

  • chrom1, start1, end1

  • chrom2, start2, end2

  • sample

  • strand1, strand2

Examples

x <- system.file("extdata/umccrise/sv/manta.vcf.gz", package = "gpgr")
sv_bedpe <- hrdetect_read_sv_vcf(x, nm = "SAMPLE")
head(sv_bedpe)
#>   chrom1    start1      end1 chrom2    start2      end2 sample strand1 strand2
#> 1   chr1   2067943   2067948   chr1   2068052   2068057 SAMPLE       +       -
#> 2   chr1  51143148  51143153   chr1  51143238  51143243 SAMPLE       +       -
#> 3   chr1  92930821  92930825   chr1  92930928  92930932 SAMPLE       +       -
#> 4   chr1  93828256  93828270   chr1  93828770  93828784 SAMPLE       +       -
#> 5   chr1 100376743 100376746   chr1 100376825 100376828 SAMPLE       +       -
#> 6   chr1 164031278 164031280   chr1 164031331 164031333 SAMPLE       +       -