Generate CCFs/gene-level calls

Two options to generate CCFs and copy number calls

1. via facets-suite

• use annotate-maf-wrapper.R to generate CCFs

• use run-facets-wrapper.R with --everything flag to generate gene/arm level calls

NOTE: Neither one is "review-aware". That is if a fit has manual reviews, then it is up to the analyst to choose the right now.

2. via facets-preview

The facets-preview package contains two functions that are "review-aware" and enable generation of genomic calls both at sample- as well as cohort-level independent of the GUI.

2.1 facetsPreview::generate_genomic_annotations

This function generate ccf.maf, gene-level and arm-level calls for every fit for a given sample. For each fit manual reviews are incorporated and the "use purity run only?", "used edited cncf", "use purity" values are taken into consideration when generating ccfs. By default, the facets_qc.txt is regenerated, although this is not always necessary. Note: mutations are expected to be in the file <sample_id>.maf in the top level directory. CCF annotation is ignored if the .maf is not found.

facetsPreview::generate_genomic_annotations(sample_id, sample_path, config_file, regenerate_qc = T)

2.2 facetsPreview::compile_cohort_annotations

Iterates through each sample in samples_to_annotate object (a data.frame/data.table with two columns: sample_id and sample_path), identifies the best fit and generates cohort level gene-level.txt, arm-level.txt and ccf.maffiles. Note that this does not generate the genomic annotations and expects as a pre-requisite that generate_genomic_annotations() is already run for each sample. A fit is identified from the facets_qc.txtwith the following order of precedence: (1) if a manually reviewed best fit is available, (2) if there is a default fit, and, if neither, (3) then choose an arbitrary fit.

This function generates four output files:

• <output_prefix>.ccf.maf

• <output_prefix>.gene_level.txt

• <output_prefix>.arm_level.txt

• <output_prefix>.cohort.txt. This file contains the fit that was chosen.

TODO: Need to allow choosing a fit independent of the facets_review. For example, through a column called selected_fit added to samples_to_annotate.

facetsPreview::compile_cohort_annotations(samples_to_annotate, output_prefix, ncores=10)