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Correct in terms of "correctly processed files" or correct true-positive variants?
What is the difference? If the files were correctly processed, doesn't it mean that I should get true-positive variants?
There is zero guarantees, and it is even extremely unlikely that all your variants will be true-positive.
You are looking for an example bam file?
How will you check if the results are correct?
Yes, I'm looking for a bam file that I know in advance the variants it should find I guess. How would you test if a varaint caller you use is giving you a sensible results and not false-positive or false-negative variants?
Search for Genome in a bottle (GIAB) data. For that sample data is freely available, together with a set of truth variants.
Truth is, there will always be false positive and false negative variants. You just have to find a pipeline which minimizes those. But in general there is always a trade-off between sensitivity and specificity: would you rather miss a variant but have high precision, or are you okay with having some false positives but with a high recall?
Great, I'll try that. thanks a lot!