CNVSomaticPairWorkflow DenoiseReadCountsNormal PoN Error
Hi, I'm running the CNVSomaticPair Workflow, and am using the gatk-recommended WGS panel of normals "cnv_somatic_PoN_4.0_WGS_for_public.pon.hdf5" which I found in the bucket...
View ArticleWhat is the plain text for an Array in Workspace Attributes
What is the plain text for an Array in Workspace Attributes? If not exist, how can I upload an array in my workspace attributes? Say I want to copy the "known_indels_array" attribute in the following...
View ArticleRunning costs on FireCloud
Hi, I'm trying to find out about how much it might cost to run a cohort of samples (500, 1000, or 2000) using germline GATK Best Practices Pipeline on FireCloud , and also how long the runs might take....
View ArticleMutect 2 on mouse cells
Hi, I am hoping to run Somatic-SNVs-Indels-GATK4 on whole exomes from a paired mouse cell lines. Just wondering where can I find the relevant intervals and reference files for this? Thanks!
View ArticleWorkflow failure dependent on FireCloud Billing Account?
I have two identical workflows (broad-firecloud-ibmwatson/CBB_20181127_CGA_WES_Characterization_TCGAControlledAccess_test and...
View ArticleMark Duplicates extremely slow in particular settings
Hi, I have about 200 subjects that I would like to run through the gatk4-data-processing/processing-for-variant-discovery-gatk4.wdl workflow. However, when arriving at the MarkDuplicates step the...
View ArticleWorkflow failure dependent on FireCloud Billing Account?
I have two identical workflows (broad-firecloud-ibmwatson/CBB_20181127_CGA_WES_Characterization_TCGAControlledAccess_test and...
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