Introduction to giptools

To run GIP is required to specify in the configuration file the path to the giptools. This is a singularity container embedding all GIP scripts and software dependencies. But giptools is more than that. GIP focus is on each individual sample, and all results (e.g. the detection of a gene amplification or a SNV) are measured with respect to the genome reference. giptools can be used to address specific questions regarding the comparisons of samples subsets (e.g. compare the gene copy number between two samples in particular).

The giptools file can be directly executed and used for the downstream comparison of samples processed by GIP. Typing giptools with no options (or with -h or –help) will list the available comparison modules. To use any of these modules the syntax is simply giptools moduleName. Each module has its own help documentation accessible with -h or –help. By default all comparison modules generate their output in the gipOut/sampleComparison folder.

gipools modules:

karyotype	Compare the chromosome sequencing coverage distributions
binCNV	Compare bin sequencing coverage in 2 samples
geCNV	Compare gene sequencing coverage in 2 samples
ternary	Compare gene sequencing coverage in 3 samples
ternaryBin	Compare bin sequencing coverage in 3 samples
SNV	Compare SNVs in multiple samples
binDensity	Density plot of bin sequencing coverage of many samples
geInteraction	Detect CNV genes in many samples and produce correlation-based networks
genomeDistance	Compare samples genomic distance
phylogeny	Extract the SNVs union and infer the phylogenetic tree
convergentCNV	Detect convergent CNV gene amplifications
overview	Overview of the sequencing coverage of chromosomes, genomic bins and genes
panel	Extract genomic information of a gene panel

All modules require as an input the --gipOut parameter specifying the GIP output folder. A description of each of the giptools modules and the available options is provided in the following pages of this documentation.

Troubleshooting

1. Read-only file system error: Depending on user’s operative system and on the singularity intallation (e.g. if it is configured to bind automatically specific directories) the user may encounter a this error. A simple workaround is to specify the host binding directory as it was done to run GIP. In this case the syntax to execute giptools modules becomes the more verbose: singularity run -B /bindDir $giptools. /bindDir is any of the upstream directory including the gipOut directory. If the gipOut directory is in your local directory you can simply use -B $PWD. $giptools is the giptools container.

2. caught segfault address (nil), cause memory not mapped: Depending on the user’s dataset the number of detected variants can be big and the default temporary directory can run out of space. Should this problem occur the user can manually specify a temporary directory. For instance mkdir -p path/to/tmpDir ; export TMPDIR=/path/to/tmpDir, then execute again the giptools module (e.g. singularity run -B /bindDir $giptools SNV)