Insertions are placed at the insertion site with a width of 1 bp; deletions span the deleted interval; INSDEL events span the affected reference region and have SVLEN=0 because the reference and alternate alleles differ in both sequence and length. Filters are available for SV type and SV length.
Where a variant falls inside an annotated tandem-repeat region, the detail page also shows the coordinates of that region (TRRBEGIN / TRREND from the source VCF), which can be useful context for repeat-mediated insertions and deletions.
-Oxford Nanopore whole-genome sequencing was performed on 3,622 Icelandic -participants enrolled through deCODE genetics. Reads were aligned to -GRCh38 and structural variants were called and merged across the cohort -following the pipeline described in Beyter et al. (2021), which combined -multiple callers and a joint reassessment of candidate variants against -the long reads. The high-confidence set released here corresponds to the -filtered callset with strong read support and consistent representation -across samples. +Beyter et al. 2021 performed Oxford Nanopore long-read sequencing of 3,622 +Icelanders recruited through deCODE genetics and detected a median of +22,636 SVs per individual (13,353 insertions and 9,474 deletions). Across +the cohort they derived a set of 133,886 reliably genotyped SV alleles, +imputed those alleles into 166,281 chip-typed Icelanders, and tested them +for association with disease and quantitative traits (notably including a +rare PCSK9 deletion associated with lower LDL-cholesterol and a +multi-allelic 57-bp VNTR in ACAN associated with adult height). The +track shown here displays the 133,886 high-confidence SV sites: 55,649 +deletions, 75,050 insertions and 3,187 combined insertion/deletion events. +The release is site-only (no per-sample genotypes or allele frequencies), +so the track cannot be filtered by AF/AC. +
++The VCF ont_sv_high_confidence_SVs.sorted.vcf.gz was downloaded +from the deCODE genetics + +LRS_SV_sets GitHub repository. +
++The step-by-step build commands (download, format conversion, bigBed build) +are recorded in the UCSC makeDoc for this track container: + +doc/hg38/lrSv.txt. The conversion scripts and autoSql schemas live in + +makeDb/scripts/lrSv.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-sep tables. From scripts, the data can be accessed through our API, track=decodeSv.
The annotation is stored as a bigBed file that can be downloaded from our download server as decodeSv.bb. Individual regions or the whole annotation can be obtained with the bigBedToBed utility, available