+This track combines the structural-variant (SV) callsets from the individual +subtracks of the Long-read SVs supertrack into a +single, position-merged overview. Each item is an SV locus seen in one or more +of the contributing long-read databases. For every merged locus the track +records which databases report it, the summed allele count across those +databases, and the range of allele frequencies observed, making it useful for +quickly seeing how widely an SV has been reported across cohorts. +
++This is a summary view. For cohort-specific genotypes, per-population allele +frequencies, and dataset-specific annotations, use the individual subtracks of +the supertrack. The merge includes the released long-read callsets only; +preliminary or unpublished subtracks (e.g. the Kim PD brain, 1000 Genomes +linear, and HPRC Jasmine sets) are not part of this merged track. +
+ ++Items are colored by SV type, matching the individual subtracks: +
+The mouseover shows the variant name, SV type, reference and insertion lengths, +the list of contributing source databases, the allele-frequency range across +those databases, and the total allele count. Filters are available for the +source database, SV type, SV length, insertion +length, total allele count, minimum and maximum allele +frequency, and the number of source databases reporting each locus. +The detail page lists the per-database allele counts. +
+ ++The merged track is built by the lrSvMergeAll.py script, which reads +the bigBed of each contributing subtrack (configured in +databases.tsv) and groups records that share an identical +(chromosome, start, end) position and SV type. For each merged locus +the script records the set of contributing databases (sources), the +number of those databases (sourceCount), the sum of their allele counts +(AC), and the minimum and maximum allele frequency across databases +that report one (minAF, maxAF). The per-database allele counts +are carried as additional columns. +
++The step-by-step build commands are recorded in the UCSC makeDoc for this track +collection: + +doc/hg38/lrSv.txt. The merge script and autoSql schema live in + +makeDb/scripts/lrSv. +
+ ++The data can be explored interactively with the +Table Browser or the +Data Integrator, and accessed +programmatically through our API, +track=lrSvAll. +
++The bigBed is available from +our +download server as lrSvAll.bb. Example: +bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/lrSv/lrSvAll.bb -chrom=chr21 -start=0 -end=100000000 stdout. +
+ ++This merged view is derived entirely from the contributing long-read SV +callsets; please see the individual subtrack description pages for the data +producers and citations for each cohort. +