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- Write a script or use a linux command to filter the output files to only contain variants that are predicted to have frequencies > 0.10 and < 0.90 or scores > 100.
- What does the
--min-alternate-totaloption mean. Experiment with using other options and examine how they affect speed versus what is predicted. Beware that some choices of options can cause crashes. - Compare the variants predicted in samples SRR032374 and SRR032376.
Run deepSNV
deepSNV runs more slowly, so we will only look at a small region of the genome initially in interactive mode. (Why is it slower? Probably in part due to using a more sophisticated statistical model and in part because it is implemented in R instead of pure C.)
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