Validating and Evaluating the Quality of an NGS pipeline

[Nilaksha]

Hello all, I'm a novice bioinformatician and have developed a NGS analysis pipeline majorly for SNP calling. I would like to evaluate the accuracy of my pipeline either against a set of genotyped SNP list or a simulated reading. I have already looked at wgsim tool, which is pretty impressive but I got doubts with the parameters of wgsim_eval.pl which are explained nowhere, even in their read me files. Any help or suggestion would be much appreciated.

Thanks

UPDATE: I found the parameter definitions for wgsim_eval.pl, they are already included in the seperate wgsim package which is not an integration of samtools, in which I found no information.

[TiborNagy]

We have used stampy's built in read simulation tool. It is well documented.

[Nilaksha]

Thanks a lot for the answer. I will read up more on that and let you know the progress