Prepare VCF with SVs for use with HRDetect

Prepares VCF with SVs for use with HRDetect.

Usage

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

Arguments

x

Path to VCF with SVs.

nm

Sample name.

genome

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

Value

Single-column data.frame (with rownames) with counts for each SV category.

Examples

x <- system.file("extdata/umccrise/sv/manta.vcf.gz", package = "gpgr")
nm <- "SampleA"
(d <- hrdetect_prep_sv(x, nm))
#>                             SampleA
#> clustered_del_1-10Kb              0
#> clustered_del_10-100Kb            0
#> clustered_del_100Kb-1Mb           0
#> clustered_del_1Mb-10Mb            0
#> clustered_del_>10Mb               0
#> clustered_tds_1-10Kb              0
#> clustered_tds_10-100Kb            0
#> clustered_tds_100Kb-1Mb           0
#> clustered_tds_1Mb-10Mb            0
#> clustered_tds_>10Mb               0
#> clustered_inv_1-10Kb              0
#> clustered_inv_10-100Kb            0
#> clustered_inv_100Kb-1Mb           0
#> clustered_inv_1Mb-10Mb            0
#> clustered_inv_>10Mb               0
#> clustered_trans                   0
#> non-clustered_del_1-10Kb          1
#> non-clustered_del_10-100Kb        0
#> non-clustered_del_100Kb-1Mb       0
#> non-clustered_del_1Mb-10Mb        2
#> non-clustered_del_>10Mb           2
#> non-clustered_tds_1-10Kb          3
#> non-clustered_tds_10-100Kb        1
#> non-clustered_tds_100Kb-1Mb       0
#> non-clustered_tds_1Mb-10Mb        1
#> non-clustered_tds_>10Mb           3
#> non-clustered_inv_1-10Kb         19
#> non-clustered_inv_10-100Kb       19
#> non-clustered_inv_100Kb-1Mb       3
#> non-clustered_inv_1Mb-10Mb        1
#> non-clustered_inv_>10Mb          10
#> non-clustered_trans              18