Variant filter - #200

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robert-a-forsyth wants to merge 28 commits into

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Commits on Sep 18, 2026

make passing variants the only form pushed through to downstream analysis in Deepvariant by default (toggleable)
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59c2216
fixes to the filtering
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c596e1b

Commits on Sep 21, 2026

testing
robert-a-forsyth
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9a1e8e6
fix bugs
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938f084

Commits on Sep 22, 2026

bump wakhan (bug)
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5b38dcf
Merge remote-tracking branch 'origin/dev' into variant_filter
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1f93364
Split multi-allelics before intersection, harden the consensus channel joins

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claude
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da99d0b
Adjudicate the tumour-only germline arm with DeepSomatic's verdict

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b646c20
Preserve the caller's FILTER through VCFTAG so the PASS filter still bites

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33bb9b2
Make the VCFTAG test runnable

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33a631b
Fold STANDARDIZE_AF into BCFTOOLS_ANNOTATE

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825af15
Drop a duplicated CLAIR3 argument and correct a false ordering comment

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d4401a4
Regenerate snapshots for the germline/somatic tagging processes

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claude
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d3b4581
Merge remote-tracking branch 'origin/dev' into variant_filter
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50d887a

Commits on Sep 23, 2026

Commits on Sep 25, 2026

Move the INFO/SOMATIC filter of local BCFTOOLS_VIEW into ext.args

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claude
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27728f8
Leave FILTER untouched in VCFTAG

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c691a0c
Prefilter DS_VERDICT_QUERY to the non-PASS/RefCall DeepSomatic rows

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75036a0
Rejoin split multi-allelics after the caller consensus

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18023f2
Join ASCAT and Wakhan report files instead of counting with groupKey

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6a3e297
Inline the PASS filter as BCFTOOLS_VIEW aliases at each caller

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d653bcb
Add VCFTAG meta.yml and fix var_keep defaults in usage.md

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c91a23e
Allow deepvariant without deepsomatic; skip the verdict transfer then

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5fae932
Cut long comments, sample numbers and CHANGELOG write-ups to one or two lines

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00a9312
Regenerate pipeline snapshots after the review fixes

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ff88896