Comments (2)
Unfortunately, the instance of the model implemented by kevlar simlike
is pretty specific to autosomal inheritance in diploid organisms. The model itself is generalizable, but I wouldn't expect this last step in the kevlar workflow to work well on plant data out-of-the-box. I'd be happy to advise on implementation and tuning, but wouldn't have much time myself to devote to it at the moment.
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The plant I am working with is a diploid plant whose seeds were mutagenized, grown, and then mated back with the parent. I would be interested in the results of simlike, even if it is not tuned well for my use case, so I am wondering at the source of the error that I attached. Please let me know if you have any ideas and I will try to resolve the code myself. I'd be happy to contribute as a branch in the future.
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Related Issues (20)
- Bug with log-space transformation
- Command or script for inspecting ambiguous calls
- MemoryError HOT 3
- Execution failed due to high FPR in case HOT 4
- Failed tests HOT 8
- Dead links to tutorial files HOT 3
- Empty files produced by kevlar split cause crash of kevlar assemble HOT 3
- python 3.6 install - pytest failures - 26 failed, 347 passed (pytest 5.3.5?) HOT 5
- Tutorial: Error on running kevlar filter HOT 9
- Clarification - how to avoid high FPR HOT 3
- kevlar memory error HOT 2
- partition, node error HOT 3
- VCF Parsing Issue HOT 1
- Where is kevlar? HOT 3
- How to just get the Kmer?
- Kevlar novel multithreading HOT 2
- count_control error: estimated false positive rate is 0.385 (FPR too high, bailing out!!! HOT 5
- > 30,000 variants reported from trio-analysis with FPR 0.001? HOT 6
- Is kevlar able to detect duplications/repeat expansions and in general CNV? HOT 1
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