Progenetix segment file format

The standard CNV segment file is a tab-delimited list, including the sample UID in the first column:

sampleID	chro	basestart	basestop	segvalue	probes
GIST-ass-15	1	0	124299999	-1	NA
GIST-ass-16	1	142400000	149599999	1	NA

Depending on the active page, the value may be the original log2 value from an array or the status marker. “Probes” will only display a value when plotting array specific data.

Please be aware that segments may be filtered out if values below the standard threshold (0.15 -0.15) are provided, or very small numbers are given for probes (leaving them empty is o.k.).