bac95a147f49cd331052e597006e04b3deee40fc max Wed Apr 22 10:43:20 2026 -0700 lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258 diff --git src/hg/makeDb/trackDb/human/onekg3202Sr.html src/hg/makeDb/trackDb/human/onekg3202Sr.html index b0bc17186ad..920bd02667a 100644 --- src/hg/makeDb/trackDb/human/onekg3202Sr.html +++ src/hg/makeDb/trackDb/human/onekg3202Sr.html @@ -1,112 +1,134 @@ <h2>Description</h2> <p> <b>This track is the only short-read dataset in the Long-Read Variants track collection; it is included for comparison with the long-read callsets.</b> </p> <p> This track shows structural variants (SVs) from the expanded 1000 Genomes Project cohort of 3,202 high-coverage <b>Illumina short-read</b> whole-genome sequences (including 602 trios), sequenced at ~30x on NovaSeq 6000 and described in Byrska-Bishop et al. 2022. SVs were called with the GATK-SV / svtools integrated pipeline; this release adds re-genotyped novel insertions and recomputed allele frequencies per continental group. </p> <p> The track contains 173,366 SVs across seven classes: 90,259 deletions (DEL), 49,693 insertions (INS), 28,242 duplications (DUP), 3,568 complex events (CPX), 920 inversions (INV), 673 multi-allelic copy-number variants (CNV) and 11 reciprocal translocations (CTX). Allele counts, allele frequencies and per-superpopulation frequencies (AFR, AMR, EAS/ASN, EUR, SAS/SAN) are provided for each site. </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> <li><span style="color: rgb(140,0,200);">Complex (CPX)</span> - purple</li> <li><span style="color: rgb(150,80,0);">Copy-number variants (CNV)</span> - brown</li> <li><span style="color: rgb(100,100,100);">Translocations (CTX)</span> - grey</li> </ul> </p> <p> Insertions are placed at the insertion site; deletions, duplications, inversions, complex and copy-number variants span the affected reference interval. Translocations show only the chr1-side breakpoint; the partner chromosome is reported on the detail page. </p> <p> Filters are available for SV type, SV length, overall allele frequency, population-max allele frequency and per-population AFs (African and European). The detail page also shows heterozygous / homozygous-alternate carrier counts, the set of upstream SV callers, the upstream pipeline source and the VCF FILTER status. </p> <h2>Methods</h2> <p> -The 1000 Genomes expanded cohort was sequenced on Illumina NovaSeq 6000 -at ~30x coverage with 2x150 bp reads. Structural variants were called -with the GATK-SV cohort pipeline and merged with svtools; novel insertions -were re-genotyped to produce the integrated callset used here -(<tt>1KGP_3202.gatksv_svtools_novelins.freeze_V3.wAF.vcf.gz</tt>). -Allele frequencies were computed genome-wide and per-population -(AFR, AMR, EAS/ASN, EUR, SAS/SAN). +Byrska-Bishop et al. 2022 sequenced the 3,202-sample expanded 1000 +Genomes Project cohort (2,504 original unrelated samples plus 698 samples +that complete 602 parent-child trios) on Illumina NovaSeq 6000 at ~30x +coverage with 2x150 bp reads. SNVs and indels were called with GATK +HaplotypeCaller. SVs were discovered and integrated from three analytic +pipelines - <a href="https://github.com/broadinstitute/gatk-sv" target="_blank"> +GATK-SV</a>, <a href="https://github.com/hall-lab/svtools" target="_blank"> +svtools</a> and Absinthe - through a machine-learning integration model; +novel insertions were re-genotyped to produce the freeze V3 callset with +added allele frequencies (<tt>*.wAF.vcf.gz</tt>). The final ensemble +callset contains 173,366 SVs across seven classes: 90,259 DELs, 49,693 +INSs, 28,242 DUPs, 920 INVs, 3,568 complex SVs (CPX), 673 multi-allelic +CNVs and 11 inter-chromosomal translocations (CTX), with AC, AN, AF and +per-superpopulation AFs (AFR, AMR, EAS/ASN, EUR, SAS/SAN). </p> <p> <b>Why a short-read track in a long-read collection?</b> Short-read SV -callsets such as this one generally have high precision for deletions -and duplications but miss many insertions, repeat expansions and -variants in complex/low-mappability regions that long-read technologies -can resolve. Displaying this callset alongside the long-read tracks in -this collection makes it easier to spot variants that are unique to -long-read data or that have substantially different breakpoints when -called from short reads. +callsets such as this one generally have high precision for deletions and +duplications but miss many insertions, repeat expansions and variants in +complex/low-mappability regions that long-read technologies can resolve. +Displaying this callset alongside the long-read tracks in this collection +makes it easier to spot variants that are unique to long-read data or +that have substantially different breakpoints when called from short +reads. +</p> +<p> +The freeze V3 VCF +<tt>1KGP_3202.gatksv_svtools_novelins.freeze_V3.wAF.vcf.gz</tt> was +downloaded from the +<a href="https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20210124.SV_Illumina_Integration/" target="_blank"> +IGSR 1000 Genomes Illumina SV integration folder</a>. +</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>. </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 accessed programmatically through our <a href="https://api.genome.ucsc.edu">API</a>, track=<i>onekg3202Sr</i>. </p> <p> The bigBed is available from <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/" target="_blank">our download server</a> as <tt>onekg3202sr.bb</tt>. Example: <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/onekg3202sr.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt>. </p> <p> The original joint-genotyped VCF is available from the <a href="https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20210124.SV_Illumina_Integration/" target="_blank"> IGSR 1000 Genomes Illumina SV integration folder</a>. </p> <h2>Credits</h2> <p> Thanks to Byrska-Bishop, Marth and the 1000 Genomes / NYGC team for releasing this dataset, and to the GATK-SV developers for the cohort calling pipeline. </p> <h2>References</h2> <p> Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K <em>et al</em>. <a href="https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(22)00991-6" target="_blank"> High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios</a>. <em>Cell</em>. 2022 Sep 1;185(18):3426-3440.e19. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36055201" target="_blank">36055201</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9439720/" target="_blank">PMC9439720</a> </p>