# gcp_gatk_mutect2_hg38
GATK mutect2 bundle for hg38 from GCP (gs://gatk-best-practices/somatic-hg38)
Recipe source code: https://github.com/rworkflow/ReUseDataRecipe/blob/master/gcp_gatk_mutect2_hg38.R (opens new window)
Data source: https://console.cloud.google.com/storage/browser/gatk-best-practices/somatic-hg38 (opens new window)
# plot
# Inputs
| label | type | description | |
|---|---|---|---|
| filename | file name | string | The file basename to download from the broad GCP bucket |
| idx | index | string? | The 'idx' or 'tbi' index file if existing |
# Outputs
| label | type | description | |
|---|---|---|---|
| gfile | gfile | File[] | The downloaded annotation files |
# Example:
gcp_gatk_mutect2_hg38 <- recipeLoad('gcp_gatk_mutect2_hg38')
gcp_gatk_mutect2_hg38$filename <- 'small_exac_common_3.hg38.vcf.gz'
gcp_gatk_mutect2_hg38$idx <- 'tbi'
getData(gcp_gatk_mutect2_hg38, outdir = 'data/folder', notes = c('gcp', 'gatk', 'mutect2', 'hg38', 'small_exac_common'))
## Get data from local catch
dataUpdate('data/folder')
dataSearch(c('gcp', 'gatk', 'hg38'))