8cf469a79d1071bd5aab4072ae0ded8ef3f418e8
lrnassar
  Thu Jun 6 17:48:00 2024 -0700
Staging the work to nest all covid tracks into a single superTrack, refs #32887

diff --git src/hg/makeDb/trackDb/human/covidHgiGwas.alpha.ra src/hg/makeDb/trackDb/human/covidHgiGwas.alpha.ra
new file mode 100644
index 0000000..eda386d
--- /dev/null
+++ src/hg/makeDb/trackDb/human/covidHgiGwas.alpha.ra
@@ -0,0 +1,92 @@
+track covidHgiGwasR4Pval
+shortLabel COVID GWAS v4
+longLabel COVID risk variants from GWAS meta-analyses by the COVID-19 Host Genetics Initiative (Rel 4, Oct 2020)
+compositeTrack on
+superTrack covid pack
+autoScale on
+maxHeightPixels 48:75:128
+type bigLolly 9 +
+lollyField 13
+mouseOver $name $ref/$alt effect $effectSize pVal $pValue studies $sourceCount
+maxItems 500000
+viewLimits 0:10
+filter.sourceCount 1
+filterLabel.sourceCount Minimum number of studies
+filter.pValueLog 3
+filter.effectSize -1.6:2.2
+filterLimits.effectSize -1.6:2.2
+filterLabel.effectSize Effect size range
+filterByRange.effectSize on
+filter._effectSizeAbs 0
+filterLabel._effectSizeAbs Minimum effect size +-
+noScoreFilter on
+bedNameLabel SNP
+priority 2
+chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22
+
+    track covidHgiGwasR4PvalA2
+    parent covidHgiGwasR4Pval on
+    shortLabel Severe COVID vars
+    longLabel Severe respiratory COVID risk variants from the COVID-19 HGI GWAS Analysis A2 (4336 cases, 12 studies, Rel 4: Oct 2020)
+    bigDataUrl /gbdb/$D/covidHgiGwas/covidHgiGwasR4.A2.$D.bb
+    priority 1
+
+    track covidHgiGwasR4PvalB2
+    parent covidHgiGwasR4Pval on
+    shortLabel Hosp COVID vars
+    longLabel Hospitalized COVID risk variants from the COVID-19 HGI GWAS Analysis B2 (7885 cases, 21 studies, Rel 4: Oct 2020)
+    bigDataUrl /gbdb/$D/covidHgiGwas/covidHgiGwasR4.B2.$D.bb
+    priority 2
+
+    track covidHgiGwasR4PvalC1
+    parent covidHgiGwasR4Pval on
+    shortLabel Tested COVID vars
+    longLabel Tested COVID risk variants from the COVID-19 HGI GWAS Analyis C1 (11085 cases, 20 studies, Rel 4: Oct 2020)
+    bigDataUrl /gbdb/$D/covidHgiGwas/covidHgiGwasR4.C1.$D.bb
+    priority 3
+
+    track covidHgiGwasR4PvalC2
+    parent covidHgiGwasR4Pval on
+    shortLabel All COVID vars
+    longLabel COVID risk variants from the COVID-19 HGI GWAS Analysis C2 (17965 cases, 33 studies, Rel 4: Oct 2020)
+    bigDataUrl /gbdb/$D/covidHgiGwas/covidHgiGwasR4.C2.$D.bb
+    priority 4
+
+track covidHgiGwas
+shortLabel COVID GWAS v3
+longLabel GWAS meta-analyses from the COVID-19 Host Genetics Initiative
+compositeTrack on
+superTrack covid hide
+autoScale on
+maxHeightPixels 48:75:128
+type bigLolly 9 +
+lollyField 21
+mouseOver $name $ref/$alt effect $effectSize pval $pValue studies $sourceCount
+maxItems 500000
+filter.sourceCount 1
+filterLabel.sourceCount Minimum number of studies
+filter.pValueLog 3
+viewLimits -13:21
+filter.effectSize -13:21
+filterLimits.effectSize -13:21
+filterLabel.effectSize Effect size range
+filterByRange.effectSize on
+filter._effectSizeAbs 0
+filterLabel._effectSizeAbs Minimum effect size +-
+noScoreFilter on
+bedNameLabel SNP
+priority 2.1
+chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22
+
+    track covidHgiGwasC2
+    parent covidHgiGwas on
+    shortLabel COVID GWAS
+    longLabel COVID GWAS from the COVID-19 Host Genetics Initiative (6696 cases, 18 studies)
+    bigDataUrl /gbdb/$D/covidHgiGwas/covidHgiGwasC2.$D.bb
+
+    track covidHgiGwasB2
+    parent covidHgiGwas off
+    shortLabel Hosp COVID GWAS
+    longLabel Hospitalized COVID GWAS from the COVID-19 Host Genetics Initiative (3199 cases, 8 studies)
+    bigDataUrl /gbdb/$D/covidHgiGwas/covidHgiGwasB2.$D.bb
+