038bd0cd3f7c84ee984905608dfdd27d02cc61ec
max
  Tue Jun 2 05:19:51 2026 -0700
[Claude] lrSv1kLin: add 1000 Genomes linear long-read SV subtrack (1,218 samples, hg38+hs1)

Two native VCFs from the Eichler lab (GRCh38 and CHM13/T2T-CHM13v2), merged
with Truvari v5.2.0 and annotated with population-level AFs (EUR, AMR, EAS,
AFR, SAS). Track is alpha-only; not added to lrSvAll -- data not yet published.
hg38: 587,779 SVs; hs1: 614,522 SVs.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

, refs #36258

diff --git src/hg/makeDb/scripts/lrSv/lrSv1kLin1218.as src/hg/makeDb/scripts/lrSv/lrSv1kLin1218.as
new file mode 100644
index 00000000000..6249d903e31
--- /dev/null
+++ src/hg/makeDb/scripts/lrSv/lrSv1kLin1218.as
@@ -0,0 +1,26 @@
+table lrSv1kLin1218
+"1000 Genomes linear long-read structural variants (1,218 samples)"
+    (
+    string chrom;              "Chromosome"
+    uint chromStart;           "Start position"
+    uint chromEnd;             "End position"
+    string name;               "Variant name"
+    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 or INS"
+    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"
+    int AC;                    "Allele Count|Number of alternate alleles observed"
+    int AN;                    "Allele Number|Total number of alleles in called genotypes"
+    float AF;                  "Allele Frequency|Overall allele frequency across all samples"
+    float afAfr;               "AF African|Allele frequency in African samples"
+    float afAmr;               "AF Admixed American|Allele frequency in Admixed American samples"
+    float afEas;               "AF East Asian|Allele frequency in East Asian samples"
+    float afEur;               "AF European|Allele frequency in European samples"
+    float afSas;               "AF South Asian|Allele frequency in South Asian samples"
+    int NS;                    "Sample Count|Number of samples with genotype data"
+    int numConsolidated;       "Consolidated Samples|Number of samples consolidated into this call by Truvari"
+    )