To install TGSim, copy the the archive with TGSim from the website, unzip it:

		unzip TumorGenomeSimulator.v1.0.zip

Compile the source code:

		make

or use the binary version (compiled for Linux 64 bit).

To run the compiled tool type:

		./tgsim -conf config.txt

You can find an example of a config file in the archive. In the config you can provide *two* fasta files to simulate a diploid genome. For example, you can introduce SNPs and short indels in hg38.fa with PIRS.

In the current version there is a fixed number and length of structural variants to add (the order is also fixed):

	addInversions(number = 3, minimal size of region = 6000, maximal size of region = 750000);
	addDuplications(number = 2,minimal size of region = 3000, maximal size of region = 10000);
	addDeletions(number = 2,minimal size of region = 10000, maximal size of region = 700000);
	duplicateGenome();
	deleteChromosomes(number = 8);
	duplicateChromosomes(number = 2);
	addTranslocations(number = 1,type = BALANCED);
	addTranslocations(number = 4,type = UNBALANCED);
	addDuplications(number = 5,minimal size of region = 3000, maximal size of region = 1200000);
	addDeletions(number = 3,minimal size of region = 100000, maximal size of region = 3000000);
	addDeletions(number = 3,minimal size of region = 3000, maximal size of region = 100000); 
	addLinkingInsertions(number = 3,minimal size of region = 4000, maximal size of region = 40000,type = DIRECT);
	addLinkingInsertions(number = 2,minimal size of region = 10000, maximal size of region = 30000,type = INVERTED);
	addReInsertions(number = 2,minimal size of region = 3000, maximal size of region = 80000,type = DIRECT);
	addReInsertions(number = 2,minimal size of region = 4000, maximal size of region = 60000,type = INVERTED);
	addDuplicationsWithInversion(number = 2,minimal size of region = 3000, maximal size of region = 40000);
	addInversions(number = 4,minimal size of region = 3000, maximal size of region = 200000);
	addSmallInsertions(number = 5,minimal size of region = 1000, maximal size of region = 2000);
	duplicateChromosomes(number = 1);
	deleteChromosomes(number = 1);
	addTranslocations(number = 1,type = UNBALANCED);
	duplicateChromosomes(number = 1);

	//add amplicons:
	addCoAmplification(number = 4,minimal size of region = 60000, maximal size of region = 80000,type = SAMECHR, number of copies = 20);
	addCoAmplification(number = 3,minimal size of region = 60000, maximal size of region = 80000,type = DIFFCHR, number of copies = 50);

If you want to modify these parameters, please, modify the main.cpp file and recompile TGSim.

Happy tumor genome simulation!

Valentina Boeva