change: drop --estimate_signatures from PCGR somatic invocation#31
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PCGR's mutational signature estimation is unreliable for our cohort and we get signature analysis from gpgr/sigrap downstream. Keep --estimate_msi and --estimate_tmb (still useful in the PCGR report). Refs: umccr/sash#57
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Pull request overview
This PR updates the PCGR somatic invocation to stop running mutational signature estimation, aligning the pipeline with current curator usage (signature analysis is handled downstream via gpgr/sigrap).
Changes:
- Remove the
--estimate_signaturesflag from the PCGR somatic command arguments. - Retain
--estimate_msiand--estimate_tmbbehind the existingdisable_estimatesswitch. - Add an inline NOTE documenting the rationale (refers to sash issue #57).
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qclayssen
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June 5, 2026 05:30
pdiakumis
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Jun 5, 2026
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Short and sweet, thank you! 👍
qclayssen
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Jul 3, 2026
Documents CI smoke tests, build fixes, split_vcf tabix-indexing, r-gpgr 2.3.1 bump, and the estimate_signatures drop (#31, sash#57) — all merged into release/0.3.0 after the v0.3.1 tag but never recorded.
This was referenced Jul 7, 2026
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PCGR's mutational signature estimation is not used by curators, we get signature analysis from gpgr/sigrap downstream.
Refs: umccr/sash#57