Coral - #205

Open

robert-a-forsyth wants to merge 38 commits into

devfrom

Commits on Sep 18, 2026

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

Commits on Sep 21, 2026

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

Commits on Sep 22, 2026

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

robert-a-forsyth
and
claude
committed
da99d0b
Adjudicate the tumour-only germline arm with DeepSomatic's verdict

robert-a-forsyth
and
claude
committed
b646c20
Preserve the caller's FILTER through VCFTAG so the PASS filter still bites

robert-a-forsyth
and
claude
committed
33bb9b2
Make the VCFTAG test runnable

robert-a-forsyth
and
claude
committed
33a631b
Fold STANDARDIZE_AF into BCFTOOLS_ANNOTATE

robert-a-forsyth
and
claude
committed
825af15
Drop a duplicated CLAIR3 argument and correct a false ordering comment

robert-a-forsyth
and
claude
committed
d4401a4
Regenerate snapshots for the germline/somatic tagging processes

robert-a-forsyth
and
claude
committed
d3b4581
Merge remote-tracking branch 'origin/dev' into variant_filter
robert-a-forsyth
committed
50d887a

Commits on Sep 23, 2026

Commits on Sep 24, 2026

Add ecDNA analysis: CoRAL reconstruction and AmpliconClassifier

robert-a-forsyth
and
claude
committed
1376557

Commits on Sep 25, 2026

fixes ecDNA subworkflow
robert-a-forsyth
committed
001926c
Move the INFO/SOMATIC filter of local BCFTOOLS_VIEW into ext.args

robert-a-forsyth
and
claude
committed
27728f8
Leave FILTER untouched in VCFTAG

robert-a-forsyth
and
claude
committed
c691a0c
Prefilter DS_VERDICT_QUERY to the non-PASS/RefCall DeepSomatic rows

robert-a-forsyth
and
claude
committed
75036a0
Rejoin split multi-allelics after the caller consensus

robert-a-forsyth
and
claude
committed
18023f2
Join ASCAT and Wakhan report files instead of counting with groupKey

robert-a-forsyth
and
claude
committed
6a3e297
Inline the PASS filter as BCFTOOLS_VIEW aliases at each caller

robert-a-forsyth
and
claude
committed
d653bcb
Add VCFTAG meta.yml and fix var_keep defaults in usage.md

robert-a-forsyth
and
claude
committed
c91a23e
Allow deepvariant without deepsomatic; skip the verdict transfer then

robert-a-forsyth
and
claude
committed
5fae932
Cut long comments, sample numbers and CHANGELOG write-ups to one or two lines

robert-a-forsyth
and
claude
committed
00a9312
Regenerate pipeline snapshots after the review fixes

robert-a-forsyth
and
claude
committed
ff88896

Commits on Sep 28, 2026

Merge remote-tracking branch 'origin/dev' into coral

ljwharbers
and
claude
committed
219aaaf
Merge dev into variant_filter

ljwharbers
and
claude
committed
7692333

Commits on Sep 29, 2026

Phase only alt somatic records, without germline records at their positions

robert-a-forsyth
and
claude
committed
46e9346
Keep one caller's record per position in the 'all' caller union

robert-a-forsyth
and
claude
committed
97801ff
Assert record contents of the phased VCFs in the pipeline tests

robert-a-forsyth
and
claude
committed
cadbdee
Warn when tumour-only DeepVariant calls run without DeepSomatic's verdict

robert-a-forsyth
and
claude
committed
24404b8
Regenerate pipeline snapshots after the review fixes

robert-a-forsyth
and
claude
committed
1982724

Commits on Sep 30, 2026

Merge remote-tracking branch 'origin/variant_filter' into coral
robert-a-forsyth
committed
9ce6a8a