FACETS copy number calling output (hg38 reference genome)

FACETS somatic copy number calling hisens (high sensitivity; cval=25) cncf .rds output from facets for each sample is stored in the .RData object Txt file contains per sample, protein coding gene level copy number calls Method: Allele specific DNA copy number inference using FACETS Total and allele-specific copy number states were inferred for all tumour samples using FACETS Suite (v 2.0.8) and FACETS (v.0.6.1) (https://github.com/mskcc/facets-suite). Tumour and matched normal bam files were pre-processed using snp-pileup (v.0.6.1) with parameters –q20 –Q20 –P100 –r25,0. A two pass implementation of FACETS using snp pileup files as input, was utilised were a low sensitivity run (cval =150) first infers the purity and log-ratio related to diploidy, as per methodology. A second higher sensitivity run (cval=25) to detect focal events, determines the copy number state of each gene. Classification of copy number (Variant_Classification Column in .txt file) were as follow: Amplification (AMP) total copy number (TCN) >= 9; Gain 3 >= TCN Deletion (DEL) TCN=0; Loss TCN=1.