[User Story] Update Sentieon

[mathiasbio]

Need

As a hospital geneticist I want:

• As many true variants as possible with as few false positive variants
• As fast as possible
• And as cheaply as possible

The new version of Sentieon: 202308 contains changes that allow us to affect all of these aspects.

Our version in production: 202010.02

Some relevant changes since version 202010.02:

• Modified TNscope® AF output format.
• Solved issue in duplex umi consensus that results depend on internal data order.
• Improved speed of bwa mem.
• Solved issue in TNscope such that evidence from overlapping read pairs were not adequately accounted for.
• Solved issue in duplex umi consensus that could output zero-length reads.
• Added support in Dedup algorithm to perform UMI barcode error correction.
• Added support in LocusCollector and Dedup algorithms to perform consensus based deduplication as well as UMI barcode aware deduplication.
• Improved machine learning model for TNscope.
• Improved consensus of INDELs in Dedup algorithm.
• Improved DNAscope pipeline speed and accuracy with a BWA model.

In summary:

• Changes to variant callers could improve accuracy and sensitivity.
• Changes to bwa mem could decrease the TAT
• Inclusion of UMIs to Dedup could save ~20% of the reads wrongly discarded as duplicates, and improve quality of reads (https://github.com/Clinical-Genomics/BALSAMIC/issues/1361)

Suggested approach

In an update Sentieon PR temporarily hard-code the changes to the path to the newest version of Sentieon:

• Ensure that all workflows are behaving as normal
• Basically perform a mini-validation in the PR, checking to see that the variant-calling is working as normal and that all files can be produced

Considered alternatives

No response

Deviation

No response

System requirements assessed

• [ ] Yes, I have reviewed the system requirements

Requirements affected by this story

No response

Risk assessment needed

• [ ] Needed
• [ ] Not needed

Risk assessment

No response

SOUPs

No response

Can be closed when

• [ ] Sentieon has been updated to most recent version, or desired new version.

Blockers

No response

Anything else?

Replaces feature issue: https://github.com/Clinical-Genomics/BALSAMIC/issues/1250