4d9c385e230b4cc8bd55815aa7ba37dea97d4c0a
max
  Mon Apr 20 08:49:42 2026 -0700
abelSv: new track for CCDG 17,795 structural variants (hg38)

Add site-frequency track for the Abel et al. 2020 Nature SV callset (PMID
32460305): 737,998 SVs from 17,795 deeply sequenced genomes. Includes the
B38 native callset (14,623 samples) and B37 lifted to hg38 (8,417 samples).
Track is colored by SV type (DEL/DUP/INV/MEI/BND) with filters for type,
callset, filter status, AC, AF, SV length, and MSQ. BND secondary mate
records are suppressed so translocation pairs appear only once.

refs #36258

diff --git src/hg/makeDb/scripts/abelSv/abelSv.as src/hg/makeDb/scripts/abelSv/abelSv.as
new file mode 100644
index 00000000000..60f057c25a2
--- /dev/null
+++ src/hg/makeDb/scripts/abelSv/abelSv.as
@@ -0,0 +1,41 @@
+table abelSv
+"Structural variants from Abel et al. 2020 (CCDG, 17,795 human genomes)"
+    (
+    string chrom;      "Chromosome"
+    uint   chromStart; "Start position"
+    uint   chromEnd;   "End position"
+    string name;       "Variant ID"
+    uint   score;      "Score (0-1000), higher AF is higher"
+    char[1] strand;    "Strand (. for most SVs)"
+    uint   thickStart; "Thick start (same as chromStart)"
+    uint   thickEnd;   "Thick end (same as chromEnd)"
+    uint   itemRgb;    "RGB color based on SV type"
+    string svType;     "SV Type|DEL=deletion, DUP=duplication, INV=inversion, MEI=mobile element insertion, BND=breakend/translocation"
+    int    svLength;   "SV Length (bp)|Difference in length between REF and ALT alleles; -1 for BND"
+    string callset;    "Source callset|B38=native GRCh38 calls (14,623 samples), B37lift=lifted from GRCh37 (8,417 samples)"
+    string filter;     "Filter status|PASS (high confidence) or LOW (low confidence)"
+    int    ac;         "Allele Count (AC)|Total alternate-allele count across all samples"
+    int    an;         "Allele Number (AN)|Total called alleles across all samples"
+    float  af;         "Allele Frequency (AF)|AC/AN"
+    float  msq;        "Mean Sample Quality (MSQ)|Mean GQ across positively genotyped samples"
+    int    nSamp;      "Samples with non-reference genotype (NSAMP)"
+    int    nFam;       "Families with non-reference genotype (NFAM)"
+    string mateChrom;  "Mate chromosome|For BND only; translocation partner"
+    int    matePos;    "Mate position|For BND only; -1 otherwise"
+    int    acAfr;      "AC - African (AFR)"
+    int    anAfr;      "AN - African (AFR)"
+    int    acAmr;      "AC - Latino/Admixed-American (AMR)"
+    int    anAmr;      "AN - Latino/Admixed-American (AMR)"
+    int    acNfe;      "AC - Non-Finnish European (NFE)"
+    int    anNfe;      "AN - Non-Finnish European (NFE)"
+    int    acFe;       "AC - Finnish European (FE)"
+    int    anFe;       "AN - Finnish European (FE)"
+    int    acEas;      "AC - East-Asian (EAS)"
+    int    anEas;      "AN - East-Asian (EAS)"
+    int    acSas;      "AC - South-Asian (SAS)"
+    int    anSas;      "AN - South-Asian (SAS)"
+    int    acPi;       "AC - Pacific Islander (PI)"
+    int    anPi;       "AN - Pacific Islander (PI)"
+    int    acOther;    "AC - Other"
+    int    anOther;    "AN - Other"
+    )