Input requirements

0. Loading a sample

At minimum only the facets run path is required to load a sample. For example, inputting the path: /juno/work/ccs/facets_runs/tumorID_normalID/, lets preview infer the sample_id as tumorID_normalID

1. Manifest file

The manifest file is required to have at least three columns with an additional column that is optional:

• sample_id column. eg: tumorID_normalID

• sample_path column. eg: /juno/work/ccs/facets_runs/tumorID_normalID/

• tumor_sample column. eg: tumorID

• dmp_id column (optional): eg: P-0000000 if the tumorID is from DMP patient P-0000000. This is only ever used to build the cBioPortal link.

2. Facets output structure

facets-preview takes only the sample_id and sample_path as input. Therefore, it relies on the specific directory structure (including specific names of directories with refits) to infer the number of files, the type of runs, etc. The default output generated by facets-suite-2.0 or higher (in --legacy-output mode only) is fully compatible with facets-preview. The following is the sample output structure (NOTE: the files that are not in blue are not required to load facets-preview):

Example command:

/juno/work/ccs/bandlamc/software/R_libs/facetsSuite/2.0.1-beta/run-facets-wrapper.R 
	--facets-lib-path /juno/work/ccs/bandlamc/software/R_libs/facets/0.5.14/ 
	--counts-file /juno/work/ccs/bandlamc/tmp/P-0007584-T01-IM5_P-0007584-N01-IM5/countsMerged____P-0007584-T01-IM5_P-0007584-N01-IM5.dat.gz
	--sample-id P-0007584-T01-IM5_P-0007584-N01-IM5
	--directory /juno/work/ccs/bandlamc/tmp/P-0007584-T01-IM5_P-0007584-N01-IM5/default/
	--snp-window-size 250 
	--normal-depth 35 
	--min-nhet 15 
	--purity-min-nhet 15 
	--seed 100
	--cval 50 
	--purity-cval 100 
	--legacy-output T 
	--genome hg19 

Example directory structure:

Example directory structure

Notes:

1. Acceptable names of the folders (containing fits) are:

   • "default"

   • "^facets.*"

   • "^refit_.*"

   • "^alt_diplogR.*"

2. facets_review.manifest contains the review information associated with the sample. The 13 columns in this file include: review_status, review_status, reviewed_by, etc. The facets_qc_version used to generate the final facets_qc call is also stored here. This allows storing facets_qc status for multiple versions of facets qc. When a sample is loaded for the first time in facets-preview, this file is automatically created.

3. facets_qc.txt has the more detailed qc metrics for each of the fits. These include statuses for the different facets qc filters along with the notes. When a sample is loaded for the first time in facets-preview, this file is automatically created.

4. *cncf.edited.txt is generated by facets-preview. See the section on Reviewing fits.

5. The *ccf.maf, *gene_level.txt and *arm_level.txt are generated for every fit by running the function facetsPreview::generate_genomic_annotations. Note: To generate CCF calls, the maf file (eg: P-0023255-T01-IM6_P-0023255-N01-IM6.maf) should exist in top level directory.

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