d8d88eb7e5c8e6df478626e5b88ee7c923c43995
max
  Sun Oct 4 09:48:15 2026 -0700
sfariSparkExomes.html: SFARI will realign and re-call the 45k WGS release (alt-aware alignment problem), the track will be updated then, refs #38424

diff --git src/hg/makeDb/trackDb/human/sfariSparkExomes.html src/hg/makeDb/trackDb/human/sfariSparkExomes.html
index 0d7df3cd6ba..96b04bf0d0f 100644
--- src/hg/makeDb/trackDb/human/sfariSparkExomes.html
+++ src/hg/makeDb/trackDb/human/sfariSparkExomes.html
@@ -5,31 +5,33 @@
 DNA samples and phenotypes. 54,558 families, parents and their children were sequenced, a total
 of 142,357 individuals with whole-exome (WES) and 12,519 with whole-genome sequencing (WGS).
 The data contains 32,559 trios and 8,895 quads (one sibling without autism), and 824 twins.
 </p>
 
 <p>
 The <a href="https://base.sfari.org/dataset/DS0000135" target="_blank">SPARK WGS August 2026
 release</a> (SFARI Base dataset DS0000135) adds whole genomes for 45,178 individuals from
 21,003 families, 20,858 of them with autism. This is a mostly new set of people: only 14 of
 them are also in the 12,519-genome release and 201 in the exome release. It includes about
 4,900 trios with an autistic child and 1,800 quads. The genomes were sequenced PCR-free on
 the Illumina NovaSeq X at Broad Clinical Labs. The track "SFARI SPARK 45k WGS ASD" shows
 this release. Its counts were computed from the genotypes, with the autism/non-autism split
 and all variants, including those seen only once. Millions of long insertions in this release
 are bacterial DNA from the saliva samples, not human variants. They are marked and hidden by
-default (see Methods).
+default (see Methods). SFARI has told us that the alignment step of this release did not
+handle the alternate haplotype sequences of GRCh38 correctly. They plan to realign the reads
+and call the variants again, and this track will be updated when the new data is available.
 </p>
 
 <p>
 The same frequencies shown here are also available publicly on the
 <a href="https://genomes.sfari.org/" target="_blank">SFARI Genome Browser</a>.
 See (SPARK et al, Neuron 2018) for details.
 </p>
 
 <h3>Phenotype-stratified counts</h3>
 <p>
 In addition to the overall allele count (AC), allele number (AN), and allele
 frequency (AF), each variant record carries counts split by autism status
 (the <tt>asd</tt> column of the SPARK individual registration file):
 </p>
 <ul>