# Reviewing a whole SV callset :::caution JBrowse v5 beta The tutorials target the JBrowse v5 beta, and the v4.3.0 release on the [download page](https://jbrowse.org/jb2/download/) lacks some of what they show. To install the beta of JBrowse Web, run `npm install -g @jbrowse/cli@next`, then `jbrowse create jbrowse2 --branch v5.0.0-beta.8`. Desktop beta builds are coming soon. ::: `jb2export batch` renders every junction in a somatic callset as a breakpoint split view, so triage becomes a directory of images. The matched normal, rendered the same way, is the control. ## Prerequisites - [`@jbrowse/img`](https://jbrowse.org/jb2/docs/jbrowse-img), which puts `jb2export` on your PATH - nothing to download: the callset, the tumor reads and the matched normal are all hosted - a JBrowse, for [the last section](#opening-a-call-in-the-browser) only ([Web](https://jbrowse.org/jb2/docs/quickstart_web) or [Desktop](https://jbrowse.org/jb2/docs/quickstart_desktop)); the renders above need none ```bash npm install -g @jbrowse/img ``` ## Where the data comes from COLO829's somatic SV callset is the ONT open-data release's own `wf-somatic-variation` run ([Valle-Inclán et al. 2022](https://doi.org/10.1016/j.xgen.2022.100139)), rehosted alongside the [cancer SV demo](https://jbrowse.org/jb2/docs/tutorials/cancer_sv). - the callset these commands fetch directly: https://jbrowse.org/demos/cancer_sv/COLO829.somatic-sv.vcf.gz - the config the batch renders read tracks from: https://jbrowse.org/demos/cancer_sv/config.json - the tumor reads the config's `COLO829_tumor_ont` track streams, Oxford Nanopore R10 from the ONT open-data release: https://ont-open-data.s3.amazonaws.com/colo829_2024.03/wf_somatic_variation/sup/COLO829_tumor.ht.cram - the matched normal the config's `COLO829BL_normal_ont` track streams: https://ont-open-data.s3.amazonaws.com/colo829_2024.03/basecalls/colo829bl/sup/PAU59807.d052sup4305mCG_5hmCGvHg38.bam ## COLO829 and its matched normal **COLO829** is a melanoma cell line with a matched normal, COLO829BL, and a community reference for somatic structural-variant calling. The [multi-hop tutorial](https://jbrowse.org/jb2/docs/tutorials/cancer_sv) follows one event in this callset all the way down; this page renders every junction at a glance. ## The contact sheet A junction joins two loci, which are the two panels of a breakpoint split view, so a callset renders straight into a review queue: ```bash curl -fO https://jbrowse.org/demos/cancer_sv/COLO829.somatic-sv.vcf.gz jb2export batch --vcf COLO829.somatic-sv.vcf.gz \ --config https://jbrowse.org/demos/cancer_sv/config.json --assembly hg38 \ --track COLO829_tumor_ont height:240 \ --outDir tumor --flank 600 --width 1100 ``` ``` Warning: skipped 35 record(s), e.g. line 271: names no second locus (INS) [########################] 100% 100/100 wrote 100/100 images to tumor ``` Insertions name one locus, so there is no second panel and the warning counts them out. Each breakend pair is written twice and collapses to one. The result is the same 100 junctions, in the same order, that `sv_multihop.py chains` reports in the [multi-hop tutorial](https://jbrowse.org/jb2/docs/tutorials/cancer_sv#finding-the-chains), because neither parses the ALT bracket by hand, which goes wrong four ways, none of them raising an error: - the replacement string may carry inserted sequence either side of the bracket (`GTGATGGATTCA[CHR12:72273112[`) - callers upper-case the mate contig, and `CHR12` is not a region hg38 has - `END=` matches inside `CIEND=`, and the first hit wins - the two records of one breakend pair name the same translocation twice One image per row, named `1_chr1_33053494-chr6_2919922_gridss12o.png`: index first so the directory sorts in callset order, coordinates next, the caller's ID last. A file with no ID column falls back to `junction_`. `--flank` frames the panel, since a breakend is one base. `--dryRun` prints the file and loci of every row and renders nothing, and `--limit 20` renders the first few, to check the framing before the whole callset. For a long run: - `--resume` skips a row whose image is already in `--outDir` - `--manifest` writes `manifest.tsv` beside the images: one row per junction with its file, both loci, its name, and whether it rendered - `--passOnly` drops records the caller filtered out. `--limit` takes the first N in file order, so on an unfiltered callset the two go together The reads stream from the hosted CRAM, the module graph loads once for the whole callset, and a `--config` URL or `--hub` is fetched once. A row that cannot be rendered is reported and the run continues. A connector drawn dashed means the read has a segment at a locus the frame does not show. These reads also visit chr10, so this junction wants a third panel, and the control belongs beside it: one render per sample, the same `--loc` list and `--width`.
`featureHeight:super-compact` draws reads at 1 px apiece, which keeps six pileups on one screen. A curve marks two loci as joined; a contig shows the order and orientation. The [multi-hop tutorial](https://jbrowse.org/jb2/docs/tutorials/cancer_sv) builds that contig from these reads, and rendering it is another `jb2export` run with a different `--assembly`. ## The same export over the normal One directory per track: ```bash jb2export batch --vcf COLO829.somatic-sv.vcf.gz \ --config https://jbrowse.org/demos/cancer_sv/config.json --assembly hg38 \ --track COLO829BL_normal_ont height:240 \ --outDir normal --flank 600 --width 1100 ``` Side by side, the somatic calls are the ones with curves in `tumor/` and none in `normal/`. ## Reading the sheet What each picture shows: - **a fan of curves at both breakends** is the junction as the reads describe it - **nothing connecting the panels** means the reads do not support the caller's coordinates, which is either a false call or a breakpoint placed far enough off that `--flank` missed it. Re-render that row wider - **curves in the normal too** means germline, not somatic - **a dense fan in a region of ragged coverage** is usually a repeat. The connectors are drawn from what the aligner reported, so a read mismapped into a repeat contributes a confident-looking curve ## Opening a call in the browser Take the coordinates from an image's filename, open the [SV inspector](https://jbrowse.org/jb2/docs/user_guides/sv_inspector_view) on the same VCF, and click through to the breakpoint split view, with the gene track and read details attached. For a junction that is one hop of something larger, the alignments track menu's **Reconstruct derivative allele...** groups the reads in view by the route their split alignments describe. COLO829's der(3) is three junctions across three chromosomes, and the [multi-hop tutorial](https://jbrowse.org/jb2/docs/tutorials/cancer_sv) follows it the rest of the way.