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GISTIC
A GISTIC file (.gistic) is the Gistic Scores File output from the GenePattern GISTIC module. It is a tab-delimited text file that defines a feature track displaying the q-value for regions of amplification or deletion found using GISTIC (Beroukhim et al., 2007). The first row contains eight column headings, which must be identical to those listed in the following table. Each subsequent row defines a GISTIC feature.
IGV displays GISTIC deletion scores as a blue line and amplification scores as a red line:
Example: scores.gistic
| Column Heading | Description |
|---|---|
| Type | Aberration type, which is specified as Amp or Del (amplification or deletion) |
| Chromosome(hg17) | Chromosome |
| Start | Location of the first base pair in the aberrant region |
| End | Location of the last base pair in the aberrant region |
| q-value | False Discovery Rate q-values for the aberrant regions (q-values below a user-defined threshold are considered significant) |
| score | G-score that considers the amplitude of the aberration as well as the frequency of its occurrence across samples |
| amplitude | Average amplitudes among aberrant samples |
| frequency | Frequency of aberration across the genome for both amplifications and deletions |