gcp_gatk_mutect2_b37

GATK mutect2 bundle for b37 from GCP (gs://gatk-best-practices/somatic-b37)
Recipe source code: https://github.com/rworkflow/ReUseDataRecipe/blob/master/gcp_gatk_mutect2_b37.R (opens new window)
Data source: https://console.cloud.google.com/storage/browser/gatk-best-practices/somatic-b37 (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_b37 <- recipeLoad('gcp_gatk_mutect2_b37')
gcp_gatk_mutect2_b37$filename <- 'small_exac_common_3.vcf'
gcp_gatk_mutect2_b37$idx <- 'idx'
getData(gcp_gatk_mutect2_b37, outdir = 'data/folder', notes = c('gcp', 'gatk', 'mutect2', 'b37', 'small_exac_common'))

## Get data from local catch
dataUpdate('data/folder')
dataSearch(c('gcp', 'gatk', 'b37'))