cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47
max
  Wed Jul 22 18:09:16 2026 -0700
lrSv cardSv: switch CARD count fields from carrier counts to allele counts

The NIH CARD provider republished the display bigBed with the count columns
changed to diploid allele counts (alleleCount = nabecAlleleCount +
hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC /
nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to
allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted
there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll
carries CARD's allele counts. refs #36258

diff --git src/hg/makeDb/scripts/lrSv/lrSvCard.as src/hg/makeDb/scripts/lrSv/lrSvCard.as
index fcde2f4c613..eefb8682540 100644
--- src/hg/makeDb/scripts/lrSv/lrSvCard.as
+++ src/hg/makeDb/scripts/lrSv/lrSvCard.as
@@ -1,20 +1,20 @@
 table lrSvCard
 "NIH CARD long-read structural variants (351 brain samples: 205 NABEC, 146 HBCC)"
     (
     string chrom;           "Chromosome"
     uint chromStart;        "Start position"
     uint chromEnd;          "End position"
     string name;            "Variant ID"
     uint score;             "Score"
     char[1] strand;         "Strand"
     uint thickStart;        "Thick start (same as chromStart)"
     uint thickEnd;          "Thick end (same as chromEnd)"
     uint reserved;          "Item color"
     string svType;          "SV Type|DEL, INS, INV or DUP"
     int svLen;              "SV Length|Length of the variant on the reference in base pairs"
     int insLen;             "Insertion Length|Length of inserted sequence, 0 for DEL/INV/DUP"
-    int AC;                 "Allele Count|Number of samples carrying this variant (genotyped carrier count)"
-    float alleleFreq;       "Allele Frequency|Fraction of samples carrying this variant (source VCF AF)"
-    uint nabecCount;        "NABEC Carriers|Carrier samples of European ancestry (NABEC cohort)"
-    uint hbccCount;         "HBCC Carriers|Carrier samples of African/African-admixed ancestry (HBCC cohort)"
+    int AC;                 "Allele Count|Alternate allele count for this variant (NABEC + HBCC)"
+    float alleleFreq;       "Allele Frequency|Alternate allele frequency (source VCF AF)"
+    uint nabecAc;           "NABEC Allele Count|Alternate allele count in the European-ancestry NABEC cohort"
+    uint hbccAc;            "HBCC Allele Count|Alternate allele count in the African/African-admixed HBCC cohort"
     )