• rongzhengqin@basepedia.com

For a particular tumor sample, CIN can be estimated by the wGII (Weighted Genomic Instability Index):

$$ wGII = \frac {\sum_{c=1}^m \sum_i^kl_i / L_c} m $$

where $p$ is the species ploidy, $m$ is the number of chromosomes, $k$ is the number of the CNV segments for each chromosome, $L_c$ is chromosome length, and $L_i$ is the length of the CNV segment.

The source code website: https://github.com/zju3351689/CINcalc

• rklib >= 1.0.0
• rblib >= 1.0.0

snippet.bash

# 1. download and install
wget https://github.com/zju3351689/CINcalc/archive/v1.0.0.tar.gz
tar zxvf v1.0.0.tar.gz
cp src/CINcalc $PATH/
chmod +x $PATH/CINcalc
 
# 2. run the script to test
$PATH/CINcalc

Usage: CINcalc.py CNVfile

Contact: Rong Zhengqin <rongzhengqin@basepedia.com>

Options:
  --version   show program's version number and exit
  -h, --help  show this help message and exit

  Required Options:
    -r FILE   chromosome size file
    -p INT    Species ploidy [2]

  Threshold Options:
    -l FLOAT  Low cutoff for loss fragments
    -u FLOAT  Up cutoff for gain fragments

• Chromosome size file

chr1	248956422
chr2	242193529
chr3	198295559

• CNV file

#SampleID               PatientID       Chromosome    Start       End             Probes   log2(CNV ratio)
TCGA-OR-A5LA-01A        TCGA-OR-A5LA    chr1          3301765     5128894         1270     -0.2177
TCGA-OR-A5LA-01A        TCGA-OR-A5LA    chr1          5132643     47878718        22491    -0.179
TCGA-OR-A5LA-01A        TCGA-OR-A5LA    chr1          47879273    109220206       36986    -0.2409
TCGA-OR-A5LA-01A        TCGA-OR-A5LA    chr1          109223247   161957073       12991    -0.1933