I have microbial whole-genome sequence (WGS) data and I want to find SNPs and INDELs if present any. Before selecting a particular aligner or variant caller for this purpose, I want to check the performance metrics (accuracy, sensitivity, precision) of different aligners and variant callers using true variant data sets or simulated datasets. So, I have the following two questions:
Is there any database from where I can get true variant data sets for microbial genome which I can use in assessing the performance metrics of different aligner or variant callers?
Which is the best tool for generating simulated data set of microbial whole-genome sequence, that I can use in assessing the performance metrics?
Apart from this, if there is any other way for analyzing the performance metrics then please do tell.
Thank you in advance.
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Prashant •
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Have you searched pubmed? By now there must be hundreds of papers that do this. Just read a few if you're uncertain which tools might work well.