Meaning of the filter column in focal copy number output

[NicolaLady]

Hi,

I am using FACETS Suite to call somatic copy number changes from whole exome seq data.

I combined all the gene_level.txt files into one for all samples to summarise the copy state for each gene across my cohort and subsequently calculate a % frequency of amps, deletions etc.

Before doing such analysis, I see there is a "filter" column in the gene_level.txt files.

What is the meaning of these filter flags? I presume i should proceed with downstream analysis using the PASS and RESCUE flags?

table(combined.genelevel$filter)

# PASS      RESCUE    suppress_large_homdel suppress_likely_unfocal_large_gain 
# 1309276      232                    13951                              51271 
# suppress_segment_too_large 
# 12644