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The sample contains a high percentage of contamination
The sample is very different from the reference genome
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How can you tune your analysis?Try different programs.
Mapping:– Change mapping parameters– Use non-unique mappings– Don’t filter duplicates
Variants:– Change variant filtration – Change variant merging – penetrance, different heredity, low coverage in one
individual…– Look for bigger variants: big insertions/ deletions, inversions, copy number
variations etc.
Gene expression:– Change the test threshold