File Changes for lrnassar
switch to commits view, user indexv500_preview to v500_preview2 (2026-06-08 to 2026-06-15) v500
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- src/hg/makeDb/doc/hg38/varFreqs.txt
- lines changed 45, context: html, text, full: html, text
af9a5b388259e680dd34bc47b2cad4ff6e3d162f Sat Jun 13 03:00:51 2026 -0700
varFreqs: pre-release polish from comprehensive sanity check.
* Sync the new combined-track shortLabels into the four description pages:
"Affected/Case Individuals" -> "Disease cohorts" and "Population + Unaffected"
-> "Population reference" (matches the trackdb shortLabels users now see).
* Add a paragraph in the supertrack Methods section describing the pooled
affectedAF / backgroundAF formulation (sum AC / sum AN) and the default_an
configuration that handles AF-only cohorts.
* Update the in-track Methods paragraphs on varFreqsAffected.html and
varFreqsBackground.html: replace "summed/maximized" with "pooled".
* Fix supertrack table downloadability column to match the underscore-prefix
convention: allofus "Yes" -> "No" (description page already says license
restricted); gregor "No" -> "Yes" (description page says VCF is on our
download server, and the gbdb path is not underscore-prefixed).
* Add a 2026-06-12 makedoc section documenting the pooled-AF rebuild, the
default_an mechanism, the new affectedAN/backgroundAN columns, the
before/after spot-check at APOE rs429358, and the build commands.
refs #36642
- src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
- lines changed 1, context: html, text, full: html, text
ae2a62a18bf9750819f17f8f2237b1f7b1b9911f Sat Jun 13 10:48:41 2026 -0700
lrSv: comment out kwanhoSv and remove all searchIndex settings. refs #36258
Per ticket: hold the preliminary/unpublished Kim PD brain track (kwanhoSv) off
dev/alpha until publication (commented out; bigBed/.as/converter/makeDoc kept),
and remove the searchIndex name settings that were added by mistake. searchIndex
removed from colorsDbSv and lrSv1kLin in lrSv.ra, from lrSvAll.ra, and from the
lrSvMergeAll.py generator so future merges do not re-add it. The pending lrSvAll
rebuild will drop KimPD from databases.tsv / the merged track.
- lines changed 3, context: html, text, full: html, text
02782ec9c99ef7f54699068afbc902e7dedccb93 Sun Jun 14 00:34:26 2026 -0700
lrSv: format the lrSvAll merged-track mouseOver as multi-line HTML. refs #36258
Replace the inline mouseOver with bold-labeled lines (Var / SV len / Ins len /
Sources / AF range / AC), in both the generated lrSvAll.ra and the
lrSvMergeAll.py generator that writes it, so a future merge regeneration
reproduces the same format.
- src/hg/makeDb/scripts/varFreqs/databases.tsv
- lines changed 6, context: html, text, full: html, text
6b285a53b036b309e3c7a9b61d3741731088a172 Fri Jun 12 02:35:01 2026 -0700
varFreqs: switch affectedAF/backgroundAF from max-across-cohorts to pooled
sum(AC)/sum(AN) so the rate matches the carrier count scale.
Per-arm AN is derived as round(AC/AF) when both are reported. An optional
"default_an" column was added to databases.tsv so AF-only cohorts (ABraOM,
ALFA) can synthesize a denominator from their cohort size; without it
those cohorts had been silently dropped from the pooled rate.
New affectedAN and backgroundAN columns expose the pool denominator. The
mouseOver now reads "Affected AC/AN: 33238 / 213153" so the ratio is
visible. Per-arm cohorts that ship only AC and no default_an (MGRB,
GREGoR AC_AFFECTED/UNAFFECTED/UNKNOWN, AllOfUs per-population) are still
listed in affectedCohorts/backgroundSources but contribute 0 to the
pool, preserving the invariant pool_AF <= 1.
The build pipeline is unchanged: re-run vcfToBigBed.py --split-affected
against the existing merged.annotated.vcf.gz. refs #36642
- src/hg/makeDb/scripts/varFreqs/vcfToBigBed.py
- lines changed 115, context: html, text, full: html, text
6b285a53b036b309e3c7a9b61d3741731088a172 Fri Jun 12 02:35:01 2026 -0700
varFreqs: switch affectedAF/backgroundAF from max-across-cohorts to pooled
sum(AC)/sum(AN) so the rate matches the carrier count scale.
Per-arm AN is derived as round(AC/AF) when both are reported. An optional
"default_an" column was added to databases.tsv so AF-only cohorts (ABraOM,
ALFA) can synthesize a denominator from their cohort size; without it
those cohorts had been silently dropped from the pooled rate.
New affectedAN and backgroundAN columns expose the pool denominator. The
mouseOver now reads "Affected AC/AN: 33238 / 213153" so the ratio is
visible. Per-arm cohorts that ship only AC and no default_an (MGRB,
GREGoR AC_AFFECTED/UNAFFECTED/UNKNOWN, AllOfUs per-population) are still
listed in affectedCohorts/backgroundSources but contribute 0 to the
pool, preserving the invariant pool_AF <= 1.
The build pipeline is unchanged: re-run vcfToBigBed.py --split-affected
against the existing merged.annotated.vcf.gz. refs #36642
- src/hg/makeDb/trackDb/human/aou1kSv.html
- lines changed 3, context: html, text, full: html, text
2e0addd016cfcbf61485b90d8980a8d75be622c2 Sun Jun 14 00:10:06 2026 -0700
lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258
After the QA dedup, update the SV counts cited on the description pages to the
unique (post-dedup) totals for the tracks served, while leaving the upstream
release/paper counts in the Methods sections:
decodeSv 133,886 -> 119,453 displayed
gustafsonSv 113,696 -> 113,159 displayed
chirmade101 87,183 -> 87,068 displayed
aou1k 541,049 -> 540,155 displayed
hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout
(no upstream publication), incl. recomputed nested-snarl counts
lrSv.html: update the Available Datasets table count cells to match, set the
lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD
Brain row, blurb and reference from the supertrack page (the track is staged on
dev/alpha only, kept out of the merge and the description, and is not released).
- src/hg/makeDb/trackDb/human/chirmade101Sv.html
- lines changed 3, context: html, text, full: html, text
2e0addd016cfcbf61485b90d8980a8d75be622c2 Sun Jun 14 00:10:06 2026 -0700
lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258
After the QA dedup, update the SV counts cited on the description pages to the
unique (post-dedup) totals for the tracks served, while leaving the upstream
release/paper counts in the Methods sections:
decodeSv 133,886 -> 119,453 displayed
gustafsonSv 113,696 -> 113,159 displayed
chirmade101 87,183 -> 87,068 displayed
aou1k 541,049 -> 540,155 displayed
hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout
(no upstream publication), incl. recomputed nested-snarl counts
lrSv.html: update the Available Datasets table count cells to match, set the
lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD
Brain row, blurb and reference from the supertrack page (the track is staged on
dev/alpha only, kept out of the merge and the description, and is not released).
- src/hg/makeDb/trackDb/human/decodeSv.html
- lines changed 3, context: html, text, full: html, text
2e0addd016cfcbf61485b90d8980a8d75be622c2 Sun Jun 14 00:10:06 2026 -0700
lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258
After the QA dedup, update the SV counts cited on the description pages to the
unique (post-dedup) totals for the tracks served, while leaving the upstream
release/paper counts in the Methods sections:
decodeSv 133,886 -> 119,453 displayed
gustafsonSv 113,696 -> 113,159 displayed
chirmade101 87,183 -> 87,068 displayed
aou1k 541,049 -> 540,155 displayed
hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout
(no upstream publication), incl. recomputed nested-snarl counts
lrSv.html: update the Available Datasets table count cells to match, set the
lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD
Brain row, blurb and reference from the supertrack page (the track is staged on
dev/alpha only, kept out of the merge and the description, and is not released).
- src/hg/makeDb/trackDb/human/gustafsonSv.html
- lines changed 3, context: html, text, full: html, text
2e0addd016cfcbf61485b90d8980a8d75be622c2 Sun Jun 14 00:10:06 2026 -0700
lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258
After the QA dedup, update the SV counts cited on the description pages to the
unique (post-dedup) totals for the tracks served, while leaving the upstream
release/paper counts in the Methods sections:
decodeSv 133,886 -> 119,453 displayed
gustafsonSv 113,696 -> 113,159 displayed
chirmade101 87,183 -> 87,068 displayed
aou1k 541,049 -> 540,155 displayed
hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout
(no upstream publication), incl. recomputed nested-snarl counts
lrSv.html: update the Available Datasets table count cells to match, set the
lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD
Brain row, blurb and reference from the supertrack page (the track is staged on
dev/alpha only, kept out of the merge and the description, and is not released).
- src/hg/makeDb/trackDb/human/hprc2v21Sv.html
- lines changed 6, context: html, text, full: html, text
2e0addd016cfcbf61485b90d8980a8d75be622c2 Sun Jun 14 00:10:06 2026 -0700
lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258
After the QA dedup, update the SV counts cited on the description pages to the
unique (post-dedup) totals for the tracks served, while leaving the upstream
release/paper counts in the Methods sections:
decodeSv 133,886 -> 119,453 displayed
gustafsonSv 113,696 -> 113,159 displayed
chirmade101 87,183 -> 87,068 displayed
aou1k 541,049 -> 540,155 displayed
hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout
(no upstream publication), incl. recomputed nested-snarl counts
lrSv.html: update the Available Datasets table count cells to match, set the
lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD
Brain row, blurb and reference from the supertrack page (the track is staged on
dev/alpha only, kept out of the merge and the description, and is not released).
- src/hg/makeDb/trackDb/human/lrSv.html
- lines changed 19, context: html, text, full: html, text
c7e0e71c357fa4630ac2ee1fb0520a32d408a1e2 Sat Jun 13 09:33:29 2026 -0700
lrSv QA round 2: alpha-gate unpublished subtracks, trim labels, fill dataset blurbs. refs #36258
Add "release alpha" to hprc2JasmineSv and lrSv1kLin so the two unpublished /
do-not-release-yet subtracks stay on dev/alpha and do not graduate with the
supertrack (both are already excluded from the lrSvAll merge via databases.tsv).
Trim three longLabels to the 85-char limit: hprc2v21Sv, hprc2JasmineSv, and
lrSv1kLin.
lrSv.html: add the missing "Available Datasets" prose blurbs for Arab APR and
CPC so all 15 datasets have a paragraph (was table-row-only).
- lines changed 36, context: html, text, full: html, text
2e0addd016cfcbf61485b90d8980a8d75be622c2 Sun Jun 14 00:10:06 2026 -0700
lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258
After the QA dedup, update the SV counts cited on the description pages to the
unique (post-dedup) totals for the tracks served, while leaving the upstream
release/paper counts in the Methods sections:
decodeSv 133,886 -> 119,453 displayed
gustafsonSv 113,696 -> 113,159 displayed
chirmade101 87,183 -> 87,068 displayed
aou1k 541,049 -> 540,155 displayed
hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout
(no upstream publication), incl. recomputed nested-snarl counts
lrSv.html: update the Available Datasets table count cells to match, set the
lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD
Brain row, blurb and reference from the supertrack page (the track is staged on
dev/alpha only, kept out of the merge and the description, and is not released).
- src/hg/makeDb/trackDb/human/lrSv.ra
- lines changed 5, context: html, text, full: html, text
c7e0e71c357fa4630ac2ee1fb0520a32d408a1e2 Sat Jun 13 09:33:29 2026 -0700
lrSv QA round 2: alpha-gate unpublished subtracks, trim labels, fill dataset blurbs. refs #36258
Add "release alpha" to hprc2JasmineSv and lrSv1kLin so the two unpublished /
do-not-release-yet subtracks stay on dev/alpha and do not graduate with the
supertrack (both are already excluded from the lrSvAll merge via databases.tsv).
Trim three longLabels to the 85-char limit: hprc2v21Sv, hprc2JasmineSv, and
lrSv1kLin.
lrSv.html: add the missing "Available Datasets" prose blurbs for Arab APR and
CPC so all 15 datasets have a paragraph (was table-row-only).
- lines changed 2, context: html, text, full: html, text
6ec6c29454ddc661b78710d1bb6de040cafaa66d Sat Jun 13 09:39:33 2026 -0700
lrSv: remove premature per-track release tags that broke tdbQuery -strict. refs #36258
The hprc2JasmineSv and lrSv1kLin stanzas carried "release alpha", but the file
is pulled in via "include lrSv.ra alpha", and tdbQuery -check -strict rejects a
stanza-level release tag when the include line already supplies a release
override ("Release tag in stanza with include release override"). The
include-level alpha already keeps the entire supertrack on dev/alpha, so these
two unpublished subtracks do not graduate regardless. Per-track release tags
for the do-not-release subtracks should be added when the include line is later
changed past alpha.
- lines changed 39, context: html, text, full: html, text
af23c5696568feae4289008ed5606a7055def77b Sat Jun 13 09:43:01 2026 -0700
lrSv: comment out the hprc2JasmineSv stanza (test callset, not for release). refs #36258
The Jasmine-merged HPRC v2 multi-caller set is a comparison/test callset that
is not slated for release, so its trackDb stanza is commented out rather than
shipped on dev/alpha. The bigBed, autoSql, converter and makeDoc are retained
for reference. The lrSv1kLin stanza is left in place pending confirmation.
- lines changed 49, context: html, text, full: html, text
ae2a62a18bf9750819f17f8f2237b1f7b1b9911f Sat Jun 13 10:48:41 2026 -0700
lrSv: comment out kwanhoSv and remove all searchIndex settings. refs #36258
Per ticket: hold the preliminary/unpublished Kim PD brain track (kwanhoSv) off
dev/alpha until publication (commented out; bigBed/.as/converter/makeDoc kept),
and remove the searchIndex name settings that were added by mistake. searchIndex
removed from colorsDbSv and lrSv1kLin in lrSv.ra, from lrSvAll.ra, and from the
lrSvMergeAll.py generator so future merges do not re-add it. The pending lrSvAll
rebuild will drop KimPD from databases.tsv / the merged track.
- lines changed 15, context: html, text, full: html, text
f09028646c6429d692a80cc38d214e805724e7fa Sat Jun 13 10:51:38 2026 -0700
lrSv: default all subtracks to hide except lrSvAll (pack), add lrSvAll desc page. refs #36258
Set the 15 released lrSv subtracks to "visibility hide" so the supertrack opens
with only the merged overview visible; lrSvAll stays "visibility pack". Add the
missing lrSvAll.html description page (Description, Display Conventions, Methods,
Data Access, Credits) describing the position-merged combined track.
- src/hg/makeDb/trackDb/human/lrSvAll.html
- lines changed 81, context: html, text, full: html, text
f09028646c6429d692a80cc38d214e805724e7fa Sat Jun 13 10:51:38 2026 -0700
lrSv: default all subtracks to hide except lrSvAll (pack), add lrSvAll desc page. refs #36258
Set the 15 released lrSv subtracks to "visibility hide" so the supertrack opens
with only the merged overview visible; lrSvAll stays "visibility pack". Add the
missing lrSvAll.html description page (Description, Display Conventions, Methods,
Data Access, Credits) describing the position-merged combined track.
- src/hg/makeDb/trackDb/human/lrSvAll.ra
- lines changed 1, context: html, text, full: html, text
ae2a62a18bf9750819f17f8f2237b1f7b1b9911f Sat Jun 13 10:48:41 2026 -0700
lrSv: comment out kwanhoSv and remove all searchIndex settings. refs #36258
Per ticket: hold the preliminary/unpublished Kim PD brain track (kwanhoSv) off
dev/alpha until publication (commented out; bigBed/.as/converter/makeDoc kept),
and remove the searchIndex name settings that were added by mistake. searchIndex
removed from colorsDbSv and lrSv1kLin in lrSv.ra, from lrSvAll.ra, and from the
lrSvMergeAll.py generator so future merges do not re-add it. The pending lrSvAll
rebuild will drop KimPD from databases.tsv / the merged track.
- lines changed 1, context: html, text, full: html, text
02782ec9c99ef7f54699068afbc902e7dedccb93 Sun Jun 14 00:34:26 2026 -0700
lrSv: format the lrSvAll merged-track mouseOver as multi-line HTML. refs #36258
Replace the inline mouseOver with bold-labeled lines (Var / SV len / Ins len /
Sources / AF range / AC), in both the generated lrSvAll.ra and the
lrSvMergeAll.py generator that writes it, so a future merge regeneration
reproduces the same format.
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 1, context: html, text, full: html, text
fa29b7e72d8fb2a9519bf14f1122feccfd79eca2 Thu Jun 11 04:46:21 2026 -0700
Retire mastermind track by gating it to alpha and noting retirement on the varsInPubs description page. refs #37753
The Genomenon Mastermind track no longer updates and the provider asked us to
take it down. Added release alpha to the mastermind subtrack so it stays on
dev/sandbox but is removed from beta and public for both hg38 and hg19, and
updated the varsInPubs.html bullet to note the track has been retired.
- lines changed 1, context: html, text, full: html, text
e211864299ad6f9570a6e28a1d4cc9044d85ec26 Sun Jun 14 00:13:00 2026 -0700
Silent release of the variant frequencies track, refs #36642
- src/hg/makeDb/trackDb/human/varFreqs.html
- lines changed 3, context: html, text, full: html, text
f0d9b9d7a69a43e62c52d80b18ef06ba1bf335ed Fri Jun 12 02:40:53 2026 -0700
varFreqs: add "tableBrowser off" to every subtrack whose bigDataUrl points
into an underscore-prefixed /gbdb dir (the rsync-exclusion convention for
non-redistributable cohorts). Covers varFreqsAffected, varFreqsBackground,
varFreqsArray, and genomeindia which were missing it.
Also fix the "Downloadable from UCSC" column on the supertrack page for
TOPMed, FinnGen and GenomeIndia (table said "Yes" but their gbdb paths
are underscore-prefixed, so they aren't actually downloadable from us).
refs #36642
- lines changed 45, context: html, text, full: html, text
af9a5b388259e680dd34bc47b2cad4ff6e3d162f Sat Jun 13 03:00:51 2026 -0700
varFreqs: pre-release polish from comprehensive sanity check.
* Sync the new combined-track shortLabels into the four description pages:
"Affected/Case Individuals" -> "Disease cohorts" and "Population + Unaffected"
-> "Population reference" (matches the trackdb shortLabels users now see).
* Add a paragraph in the supertrack Methods section describing the pooled
affectedAF / backgroundAF formulation (sum AC / sum AN) and the default_an
configuration that handles AF-only cohorts.
* Update the in-track Methods paragraphs on varFreqsAffected.html and
varFreqsBackground.html: replace "summed/maximized" with "pooled".
* Fix supertrack table downloadability column to match the underscore-prefix
convention: allofus "Yes" -> "No" (description page already says license
restricted); gregor "No" -> "Yes" (description page says VCF is on our
download server, and the gbdb path is not underscore-prefixed).
* Add a 2026-06-12 makedoc section documenting the pooled-AF rebuild, the
default_an mechanism, the new affectedAN/backgroundAN columns, the
before/after spot-check at APOE rs429358, and the build commands.
refs #36642
- src/hg/makeDb/trackDb/human/varFreqs.ra
- lines changed 2, context: html, text, full: html, text
dce21104b16337c132dea98bc763d74313381101 Fri Jun 12 01:05:02 2026 -0700
varFreqs: rename combined-track shortLabels per the conversation with Max
on the ticket. varFreqsAffected -> "Disease cohorts" (was "Affected/Case
Individuals"); varFreqsBackground -> "Population reference" (was
"Population + Unaffected"). longLabels unchanged. refs #36642
- lines changed 14, context: html, text, full: html, text
6b285a53b036b309e3c7a9b61d3741731088a172 Fri Jun 12 02:35:01 2026 -0700
varFreqs: switch affectedAF/backgroundAF from max-across-cohorts to pooled
sum(AC)/sum(AN) so the rate matches the carrier count scale.
Per-arm AN is derived as round(AC/AF) when both are reported. An optional
"default_an" column was added to databases.tsv so AF-only cohorts (ABraOM,
ALFA) can synthesize a denominator from their cohort size; without it
those cohorts had been silently dropped from the pooled rate.
New affectedAN and backgroundAN columns expose the pool denominator. The
mouseOver now reads "Affected AC/AN: 33238 / 213153" so the ratio is
visible. Per-arm cohorts that ship only AC and no default_an (MGRB,
GREGoR AC_AFFECTED/UNAFFECTED/UNKNOWN, AllOfUs per-population) are still
listed in affectedCohorts/backgroundSources but contribute 0 to the
pool, preserving the invariant pool_AF <= 1.
The build pipeline is unchanged: re-run vcfToBigBed.py --split-affected
against the existing merged.annotated.vcf.gz. refs #36642
- lines changed 4, context: html, text, full: html, text
f0d9b9d7a69a43e62c52d80b18ef06ba1bf335ed Fri Jun 12 02:40:53 2026 -0700
varFreqs: add "tableBrowser off" to every subtrack whose bigDataUrl points
into an underscore-prefixed /gbdb dir (the rsync-exclusion convention for
non-redistributable cohorts). Covers varFreqsAffected, varFreqsBackground,
varFreqsArray, and genomeindia which were missing it.
Also fix the "Downloadable from UCSC" column on the supertrack page for
TOPMed, FinnGen and GenomeIndia (table said "Yes" but their gbdb paths
are underscore-prefixed, so they aren't actually downloadable from us).
refs #36642
- lines changed 31, context: html, text, full: html, text
21e8af7d071bb2294f0cf682ac871c63a5a5332d Sat Jun 13 05:00:09 2026 -0700
varFreqs: reorder subtrack priorities A-Z by shortLabel.
Combined tracks keep their order: Population reference (0.1), Disease cohorts
(0.11), Genotyping Array Databases Combined (0.2). The 32 per-project
subtracks get integer priorities 1..32 sorted alphabetically by shortLabel
(case-insensitive). Adds explicit priority to the 9 subtracks that lacked
one (abraom, gasp, gaspIndel, hrc, indigenomes, kova, mgrb, npm, saudi).
refs #36642
- lines changed 1, context: html, text, full: html, text
c6c684b4d0ec1926eb07485b899b0f48496f7063 Sat Jun 13 05:30:17 2026 -0700
varFreqs: add a "New" pennantIcon to the supertrack as a placeholder
pointing to newsarch.html#TBD. Once the release news post lands, update the
anchor and tooltip with the actual date. refs #36642
- src/hg/makeDb/trackDb/human/varFreqsAffected.html
- lines changed 19, context: html, text, full: html, text
6b285a53b036b309e3c7a9b61d3741731088a172 Fri Jun 12 02:35:01 2026 -0700
varFreqs: switch affectedAF/backgroundAF from max-across-cohorts to pooled
sum(AC)/sum(AN) so the rate matches the carrier count scale.
Per-arm AN is derived as round(AC/AF) when both are reported. An optional
"default_an" column was added to databases.tsv so AF-only cohorts (ABraOM,
ALFA) can synthesize a denominator from their cohort size; without it
those cohorts had been silently dropped from the pooled rate.
New affectedAN and backgroundAN columns expose the pool denominator. The
mouseOver now reads "Affected AC/AN: 33238 / 213153" so the ratio is
visible. Per-arm cohorts that ship only AC and no default_an (MGRB,
GREGoR AC_AFFECTED/UNAFFECTED/UNKNOWN, AllOfUs per-population) are still
listed in affectedCohorts/backgroundSources but contribute 0 to the
pool, preserving the invariant pool_AF <= 1.
The build pipeline is unchanged: re-run vcfToBigBed.py --split-affected
against the existing merged.annotated.vcf.gz. refs #36642
- lines changed 7, context: html, text, full: html, text
af9a5b388259e680dd34bc47b2cad4ff6e3d162f Sat Jun 13 03:00:51 2026 -0700
varFreqs: pre-release polish from comprehensive sanity check.
* Sync the new combined-track shortLabels into the four description pages:
"Affected/Case Individuals" -> "Disease cohorts" and "Population + Unaffected"
-> "Population reference" (matches the trackdb shortLabels users now see).
* Add a paragraph in the supertrack Methods section describing the pooled
affectedAF / backgroundAF formulation (sum AC / sum AN) and the default_an
configuration that handles AF-only cohorts.
* Update the in-track Methods paragraphs on varFreqsAffected.html and
varFreqsBackground.html: replace "summed/maximized" with "pooled".
* Fix supertrack table downloadability column to match the underscore-prefix
convention: allofus "Yes" -> "No" (description page already says license
restricted); gregor "No" -> "Yes" (description page says VCF is on our
download server, and the gbdb path is not underscore-prefixed).
* Add a 2026-06-12 makedoc section documenting the pooled-AF rebuild, the
default_an mechanism, the new affectedAN/backgroundAN columns, the
before/after spot-check at APOE rs429358, and the build commands.
refs #36642
- src/hg/makeDb/trackDb/human/varFreqsArray.html
- lines changed 5, context: html, text, full: html, text
af9a5b388259e680dd34bc47b2cad4ff6e3d162f Sat Jun 13 03:00:51 2026 -0700
varFreqs: pre-release polish from comprehensive sanity check.
* Sync the new combined-track shortLabels into the four description pages:
"Affected/Case Individuals" -> "Disease cohorts" and "Population + Unaffected"
-> "Population reference" (matches the trackdb shortLabels users now see).
* Add a paragraph in the supertrack Methods section describing the pooled
affectedAF / backgroundAF formulation (sum AC / sum AN) and the default_an
configuration that handles AF-only cohorts.
* Update the in-track Methods paragraphs on varFreqsAffected.html and
varFreqsBackground.html: replace "summed/maximized" with "pooled".
* Fix supertrack table downloadability column to match the underscore-prefix
convention: allofus "Yes" -> "No" (description page already says license
restricted); gregor "No" -> "Yes" (description page says VCF is on our
download server, and the gbdb path is not underscore-prefixed).
* Add a 2026-06-12 makedoc section documenting the pooled-AF rebuild, the
default_an mechanism, the new affectedAN/backgroundAN columns, the
before/after spot-check at APOE rs429358, and the build commands.
refs #36642
- src/hg/makeDb/trackDb/human/varFreqsBackground.html
- lines changed 23, context: html, text, full: html, text
6b285a53b036b309e3c7a9b61d3741731088a172 Fri Jun 12 02:35:01 2026 -0700
varFreqs: switch affectedAF/backgroundAF from max-across-cohorts to pooled
sum(AC)/sum(AN) so the rate matches the carrier count scale.
Per-arm AN is derived as round(AC/AF) when both are reported. An optional
"default_an" column was added to databases.tsv so AF-only cohorts (ABraOM,
ALFA) can synthesize a denominator from their cohort size; without it
those cohorts had been silently dropped from the pooled rate.
New affectedAN and backgroundAN columns expose the pool denominator. The
mouseOver now reads "Affected AC/AN: 33238 / 213153" so the ratio is
visible. Per-arm cohorts that ship only AC and no default_an (MGRB,
GREGoR AC_AFFECTED/UNAFFECTED/UNKNOWN, AllOfUs per-population) are still
listed in affectedCohorts/backgroundSources but contribute 0 to the
pool, preserving the invariant pool_AF <= 1.
The build pipeline is unchanged: re-run vcfToBigBed.py --split-affected
against the existing merged.annotated.vcf.gz. refs #36642
- lines changed 6, context: html, text, full: html, text
af9a5b388259e680dd34bc47b2cad4ff6e3d162f Sat Jun 13 03:00:51 2026 -0700
varFreqs: pre-release polish from comprehensive sanity check.
* Sync the new combined-track shortLabels into the four description pages:
"Affected/Case Individuals" -> "Disease cohorts" and "Population + Unaffected"
-> "Population reference" (matches the trackdb shortLabels users now see).
* Add a paragraph in the supertrack Methods section describing the pooled
affectedAF / backgroundAF formulation (sum AC / sum AN) and the default_an
configuration that handles AF-only cohorts.
* Update the in-track Methods paragraphs on varFreqsAffected.html and
varFreqsBackground.html: replace "summed/maximized" with "pooled".
* Fix supertrack table downloadability column to match the underscore-prefix
convention: allofus "Yes" -> "No" (description page already says license
restricted); gregor "No" -> "Yes" (description page says VCF is on our
download server, and the gbdb path is not underscore-prefixed).
* Add a 2026-06-12 makedoc section documenting the pooled-AF rebuild, the
default_an mechanism, the new affectedAN/backgroundAN columns, the
before/after spot-check at APOE rs429358, and the build commands.
refs #36642
- src/hg/makeDb/trackDb/human/varsInPubs.html
- lines changed 3, context: html, text, full: html, text
fa29b7e72d8fb2a9519bf14f1122feccfd79eca2 Thu Jun 11 04:46:21 2026 -0700
Retire mastermind track by gating it to alpha and noting retirement on the varsInPubs description page. refs #37753
The Genomenon Mastermind track no longer updates and the provider asked us to
take it down. Added release alpha to the mastermind subtrack so it stays on
dev/sandbox but is removed from beta and public for both hg38 and hg19, and
updated the varsInPubs.html bullet to note the track has been retired.
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