We recently tried to use SCNVSim to create some simulated datasets and encountered the following problems, noting here for the benefit of others:
1) There is no way to specify a seed in order to reproduce the generated dataset.
2) It appears that the generated SNVs are inserted into the normal genome, but are not being inserted into the tumor genome (this is after viewing alignment pileups of reads simulated from the respective genomes
3) The generated SNV/indels VCF file is not valid VCF - it is missing a header and uses illegal method to represent insertions and deletions, which prevents use with other VCF tools (e.g. loading into IGV) without much munging required.
4) Once when we ran the program it entered an infinite loop in the while loop near the start of ChromExchanger.generateRandomITX()
5) There are no unit tests, which does not inspire confidence in the tools.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
We recently tried to use SCNVSim to create some simulated datasets and encountered the following problems, noting here for the benefit of others:
1) There is no way to specify a seed in order to reproduce the generated dataset.
2) It appears that the generated SNVs are inserted into the normal genome, but are not being inserted into the tumor genome (this is after viewing alignment pileups of reads simulated from the respective genomes
3) The generated SNV/indels VCF file is not valid VCF - it is missing a header and uses illegal method to represent insertions and deletions, which prevents use with other VCF tools (e.g. loading into IGV) without much munging required.
4) Once when we ran the program it entered an infinite loop in the while loop near the start of ChromExchanger.generateRandomITX()
5) There are no unit tests, which does not inspire confidence in the tools.