# 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

## gcp_gatk_mutect2_hg38

# 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:

recipeLoad('gcp_gatk_mutect2_hg38', return = TRUE)
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', 'broad', 'mutect2', 'small_exac_common'))