segmentation algorithm.  (See GLAD file format in the Genepattern

file formats documentation.)  It is a six column, tab-delimited

file with an optional first line identifying the columns.

Positions are in base pair units.The column headers are: (1)

Sample (sample name), (2) Chromosome (chromosome number), (3)

Start Position (segment start position, in bases), (4) End

Position (segment end position, in bases), (5) Num markers (number

of markers in segment), (6) Seg.CN (log2() -1 of copy number).

Markers File: The markers file identifies the marker names and

positions of the markers in the original dataset (before

segmentation). It is a three column, tab-delimited file with an

optional header. The column headers are: (1) Marker Name, (2)

Chromosome, (3) Marker Position (in bases).

Reference Genome: The reference genome file contains information

about the location of genes and cytobands on a given build of the

genome. Reference genome files are created in Matlab and are

CNV Files: There are two options for the cnv file. The first

option allows CNVs to be identified by marker name. The second

option allows the CNVs to be identified by genomic location.

Option #1: A two column, tab-delimited file with an optional

header row. The marker names given in this file must match the

marker names given in the markers file. The CNV identifiers are

for user use and can be arbitrary. The column headers are: (1)

Marker Name, (2) CNV Identifier. Option #2: A 6 column,

tab-delimited file with an optional header row. The

'CNV Identifier' is for user use and can be arbitrary. 'Narrow

Region Start' and 'Narrow Region End' are also not used. The

column headers are: (1) CNV Identifier, (2) Chromosome, (3)

Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start,

Amplification Threshold: Threshold for copy number amplifications.

Regions with a log2 ratio above this value are considered

Deletion Threshold: Threshold for copy number deletions. Regions

with a log2 ratio below the negative of this value are considered