Clinical-Genomics
[User Story] Update TIDDIT to make use of single-end reads
Need
As a clinician I want to detect as many true SVs as possible. After the update planned in balsamic 16.0.0 we're going to have a lot more single-end reads in our bam files due to the UMI collapse implemented here: https://github.com/Clinical-Genomics/BALSAMIC/pull/1358
In a a recent version of TIDDIT there has been an update that greatly improves the use of single end reads in SV variant calling: https://github.com/SciLifeLab/TIDDIT/releases
It seems then like an opportune time to update TIDDIT as a part of release 16.
Suggested approach
Update TIDDIT and implement in release 16.
Test the new version in the new deduplicate with UMIs branch: https://github.com/Clinical-Genomics/BALSAMIC/pull/1358
Considered alternatives
No response
Deviation
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System requirements assessed
- [ ] Yes, I have reviewed the system requirements
Requirements affected by this story
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Risk assessment needed
- [ ] Needed
- [ ] Not needed
Risk assessment
No response
SOUPs
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Can be closed when
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Blockers
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Anything else?
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I opened an issue for the package to be uploaded to Bioconda: https://github.com/SciLifeLab/TIDDIT/issues/119.
I reviewed the errors and it seems there's a bug in the TIDDIT code. However, I'm not very familiar with Bioconda recipes. I also encountered a similar error with Cython when attempting to install it from scratch.
