9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 lrnassar Mon Jun 29 14:21:07 2026 -0700 lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released). diff --git src/hg/makeDb/trackDb/human/ga4kSv.html src/hg/makeDb/trackDb/human/ga4kSv.html index 1f6ef9d049e..32bf358d186 100644 --- src/hg/makeDb/trackDb/human/ga4kSv.html +++ src/hg/makeDb/trackDb/human/ga4kSv.html @@ -1,118 +1,118 @@ <h2>Description</h2> <p> This track shows structural variants (SVs) identified by PacBio HiFi long-read sequencing of probands and their families enrolled in the Genomic Answers for Kids (GA4K) program at Children's Mercy Research Institute. GA4K is a longitudinal pediatric genomics initiative that aims to enroll 30,000 children with suspected rare genetic disorders, together with their parents, to build a large-scale resource of clinical and genomic data. </p> <p> The callset contains 115,554 SVs (52,564 deletions, 58,219 insertions, 4,408 duplications, 363 inversions) from 502 sequenced samples. Variants are site-level (no per-sample genotypes) and each SV has been replicated, meaning that it was either observed in two or more unrelated GA4K individuals, or matched an SV from an external long-read reference set (Decode or the Human Pangenome Reference Consortium). </p> <h2>Display Conventions and Configuration</h2> <p> Items are colored by SV type: <ul> <li><span style="color: rgb(200,0,0);">Deletions (DEL)</span> - red</li> <li><span style="color: rgb(0,0,200);">Insertions (INS)</span> - blue</li> <li><span style="color: rgb(0,160,0);">Duplications (DUP)</span> - green</li> <li><span style="color: rgb(230,140,0);">Inversions (INV)</span> - orange</li> </ul> </p> <p> Insertions are placed at the insertion site with a width of 1 bp; deletions, duplications and inversions span the affected interval. Filters are available for SV type, SV length, carrier-sample count and allele frequency. The detail page also shows the total number of samples genotyped at each site. </p> <h2>Methods</h2> <p> The Genomic Answers for Kids (GA4K) program at Children's Mercy Research Institute is a longitudinal pediatric rare-disease initiative described in Cohen et al. 2022. GA4K probands and their families are sequenced with PacBio HiFi long reads (Revio and Sequel II), and the 502-sample GA4K PacBio SV release (<tt>pb_joint_merged.sv.vcf.gz</tt>) is produced by running <a href="https://github.com/PacificBiosciences/pbsv" target="_blank"> pbsv</a> per sample and merging with <a href="https://github.com/mkirsche/Jasmine" target="_blank">JASMINE</a> v1.1.4 (<tt>--output-genotypes</tt>). The merged site-level VCF is filtered to SVs replicated in at least two independent observations (either matching a second unrelated CMH individual in the same Jasmine cluster, or matching an SV in the deCODE Icelandic or HPRC callsets via <a href="https://github.com/PacificBiosciences/svpack" target="_blank"> svpack match</a>). The released catalog contains 115,554 replicated SVs (52,564 deletions, 58,219 insertions, 4,408 duplications and 363 inversions) with recomputed carrier counts (SVC), total sample counts (SVN) and allele frequencies (SVF = SVC/SVN). </p> <p> The source VCF was cloned from the Children's Mercy Research Institute GA4K GitHub repository, <a href="https://github.com/ChildrensMercyResearchInstitute/GA4K" target="_blank"> github.com/ChildrensMercyResearchInstitute/GA4K</a> (<tt>pacbio_sv_vcf/pb_joint_merged.sv.vcf.gz</tt>). </p> <p> The step-by-step build commands (download, format conversion, bigBed build) are recorded in the UCSC makeDoc for this track container: <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/lrSv.txt" target="_blank"> doc/hg38/lrSv.txt</a>. The conversion scripts and autoSql schemas live in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/lrSv" target="_blank"> -makeDb/scripts/lrSv</a>. +makeDb/scripts/lrSv</a>, and the track configuration is in <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/lrSv.ra" target="_blank">trackDb/human/lrSv.ra</a>. </p> <h2>Data Access</h2> <p> The data can be explored interactively in table format with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there to spreadsheet or tab-sep tables. From scripts, the data can be accessed through our <a href="https://api.genome.ucsc.edu">API</a>, track=<i>ga4kSv</i>. </p> <p> For automated download and analysis, the annotation is stored in a bigBed file that can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/" target="_blank">our download server</a>. The file for this track is called <tt>ga4kSv.bb</tt>. Individual regions or the whole annotation can be obtained using the <tt>bigBedToBed</tt> utility, available as a precompiled binary or from source as described on our <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">utilities page</a>. Example: <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/ga4kSv.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt>. </p> <p> The original VCF is available from the Children's Mercy Research Institute GA4K data release at <a href="https://github.com/ChildrensMercyResearchInstitute/GA4K" target="_blank"> github.com/ChildrensMercyResearchInstitute/GA4K</a>. </p> <h2>Credits</h2> <p> Thanks to the Children's Mercy Research Institute and the Genomic Answers for Kids participants and their families for making this dataset publicly available. </p> <h2>References</h2> <p> Cohen ASA, Farrow EG, Abdelmoity AT, Alaimo JT, Amudhavalli SM, Anderson JT, Bansal L, Bartik L, Baybayan P, Belden B <em>et al</em>. <a href="https://linkinghub.elsevier.com/retrieve/pii/S1098-3600(22)00653-0" target="_blank"> Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes</a>. <em>Genet Med</em>. 2022 Jun;24(6):1336-1348. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35305867" target="_blank">35305867</a> </p>