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I just wrote a walker to look for particular types of low frequency mutations, and I wanted to verify that the methods were working. I was hoping to simulate some illumina data with the variants and then run the methods against this data.
However, I don't know what a realistic error model is for common Illumina data and so am not sure how realistic my simulations are (Proportion of gaps, A->C versus A->G, etc.). Does the GATK include a read simulator? I saw one walker in the documentation but it seemed to rely on inputting settings that I didn't know about it and looked a bit out of date.
Any help appreciated.