R08.06.01.02 · 任务小类

基因组浏览器与变异检查

Genome browser & variant inspection

Load tracks and judge variants and coverage visually.

20 条本项目编写的提案 · 分类 v1.1 · 新增基准运行 0 次。下方验证方式与部分得分规则是设计，不是执行结果。

典型应用: IGV · UCSC Genome Browser
小类 GUI 需求标签: HY · 混合

任务提案 · 20

展开查看完整原文与建议检查方式；两种界面均保留提案英文原文。

R08.06.01.02-T01 Classify five variants as real or artifact by read-level inspection in IGV

原始指令

In IGV desktop load input/hg38 genome, input/sample.bam and input/calls.vcf. For each of the five variants in calls.vcf, inspect read support (strand balance, mapping quality, soft clips, position in read, duplicates) and label it 'true' or 'artifact' with a one-phrase reason in output/labels.csv.

平台: mac · macOS win · Windows lin · Linux
应用: IGV
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 nav · 平移 / 缩放 / 滚动 vis · 视觉判断 hover · 悬停与上下文
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 3 / 5

建议验证方式

Labels must match gold for all five (gold from orthogonal validation); reasons keyword-checked against the seeded defect per site (strand bias, low MAPQ, soft-clip cluster, duplicate stack).

建议部分得分

80% correct labels (16 pts each); 20% reasons matching the seeded causes.

R08.06.01.02-T02 Confirm a 12 kb heterozygous deletion in IGV and report its breakpoints

原始指令

In IGV load input/sample.bam over chr7:117,100,000-117,400,000 with coverage and pair orientation colouring. Find the heterozygous deletion indicated by larger-than-expected insert sizes and halved coverage, and report its breakpoints to the nearest 100 bp plus supporting read-pair count in output/answer.json. Save the session as output/del.xml.

平台: mac · macOS win · Windows lin · Linux
应用: IGV
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: nav · 平移 / 缩放 / 滚动 click · 指向与点击 vis · 视觉判断
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 4 / 5

建议验证方式

Both breakpoints within 200 bp of gold; supporting pair count within 20% of the reference count; session must show the BAM with insert-size colouring in the region. No SV VCF is provided. samtools, pysam and SV callers are not installed on the VM, so evidence must be read in IGV, and the session must show the inspected region.

建议部分得分

35% start breakpoint; 35% end breakpoint; 20% support count; 10% session saved.

R08.06.01.02-T03 Count canonical BRCA2 exons in the UCSC Genome Browser

原始指令

In the UCSC Genome Browser (hg38) navigate to BRCA2 with GENCODE in full mode, identify the MANE Select transcript and report its exon count, chromosome span and strand in output/answer.json.

平台: web · 任意系统（网页）
应用: UCSC Genome Browser
交互表面: brow · 浏览器
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 nav · 平移 / 缩放 / 滚动 hover · 悬停与上下文
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 2 / 5

建议验证方式

Exon count, span (within 10 bp) and strand must equal the MANE Select record for BRCA2 in hg38.

建议部分得分

50% exon count; 30% span; 20% strand.

R08.06.01.02-T04 Export a TP53 locus browser view with SV and histone tracks as SVG

原始指令

In the local UCSC mirror (Genome Browser in a Box, hg19) go to chr17:7,571,651-7,590,910 and add the tabix VCF and the bigWig served at the fixture URLs in input/urls.txt as custom tracks, set GENCODE to pack, hide default regulation tracks, and export the view as output/output.svg with both custom tracks visible.

平台: web · 任意系统（网页）
应用: UCSC Genome Browser · Genome Browser in a Box
交互表面: brow · 浏览器
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 type · 文字与表单 nav · 平移 / 缩放 / 滚动
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 3 / 5

建议验证方式

SVG must contain both custom track labels, the coordinate range in the title, a signal path whose peak x-positions match the bigWig maxima within 2% of the image width, and GENCODE in pack mode.

建议部分得分

30% both custom tracks present; 25% coordinates; 25% signal consistent with data; 20% track modes.

R08.06.01.02-T05 Inspect exome coverage and list exons needing resequencing in IGV

原始指令

In IGV load input/exome.bam and input/panel_exons.bed over the 12 exons of the gene panel. Using coverage inspection, list in output/lowcov.csv every exon where coverage falls below 20× across more than 10% of its length, with the approximate low region.

平台: mac · macOS win · Windows lin · Linux
应用: IGV
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 hover · 悬停与上下文
工作产物: WP02 · 记录 / 表格
条件: 未声明
提案难度: 3 / 5

建议验证方式

Exon set must equal gold (computed with samtools depth); each reported low region must overlap the gold low region with IoU ≥0.5.

建议部分得分

60% exon set exact (scaled); 40% low regions localized.

R08.06.01.02-T06 Determine the phase of two nearby variants from read pairs in IGV

原始指令

In IGV load input/trio_child.bam and view the two heterozygous variants listed in input/vars.txt (320 bp apart). Using reads and pairs that span both, decide whether they are in cis or trans, and report the call with the counts of reads supporting each haplotype in output/answer.json.

平台: mac · macOS win · Windows lin · Linux
应用: IGV
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 click · 指向与点击
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 4 / 5

建议验证方式

Phase call must equal gold (from long-read phasing); haplotype read counts within 15% of reference counts. No phased VCF or HP tags are present; phasing tools, samtools and pysam are absent from the image, and IGV's batch port is disabled.

建议部分得分

60% phase call; 40% supporting counts.

R08.06.01.02-T07 Save a UCSC session with a custom BED, GENCODE full and conservation hidden

原始指令

In the UCSC Genome Browser (hg38) upload input/peaks.bed as a custom track, set it to pack, GENCODE to full, hide the Conservation track, navigate to chr8:127,700,000-127,760,000 and save a named session 'fc_session_01' in the sandbox account. Write the session URL to output/session.txt.

平台: web · 任意系统（网页）
应用: UCSC Genome Browser
交互表面: brow · 浏览器
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 type · 文字与表单 nav · 平移 / 缩放 / 滚动
工作产物: WP08 · 应用 / 系统状态
条件: 未声明
提案难度: 2 / 5

建议验证方式

Fetching the session settings must show the custom track in pack with the uploaded peaks, GENCODE full, Conservation hidden and the stated position (within 1 kb).

建议部分得分

30% custom track uploaded; 30% track visibility settings; 20% position; 20% session saved and shared.

R08.06.01.02-T08 Find the misannotated transcript isoform from RNA-seq coverage in IGV

原始指令

In IGV load input/rnaseq.bam (with splice junctions), input/gencode.gtf and the four candidate transcripts of the gene in input/candidates.txt. Decide which annotated isoform the data actually support, and report it plus the two junctions that exclude the others in output/answer.json. Save output/isoform.xml.

平台: mac · macOS win · Windows lin · Linux
应用: IGV
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 hover · 悬停与上下文
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 4 / 5

建议验证方式

Isoform ID must equal gold; both junctions must match gold coordinates within 2 bp and have ≥10 supporting reads in the BAM. Quantification and junction tools (salmon, StringTie, regtools), samtools and pysam are not installed in the image.

建议部分得分

50% isoform; 40% two junctions; 10% session saved.

R08.06.01.02-T09 Build a JBrowse 2 session with three tracks and export its session JSON

原始指令

In JBrowse 2 (web, local server) with the hg38 assembly, add input/sample.cram, input/variants.vcf.gz and input/coverage.bw as tracks, open a linear genome view at chr12:25,200,000-25,260,000 with the alignments sorted by base at the KRAS G12 codon, and export the session to output/session.json.

平台: web · 任意系统（网页）
应用: JBrowse 2
交互表面: brow · 浏览器
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 type · 文字与表单 nav · 平移 / 缩放 / 滚动
工作产物: WP08 · 应用 / 系统状态
条件: tutorial · 阅读文档 / 教程
提案难度: 3 / 5

建议验证方式

session.json must declare the three tracks with the given adapters, the view locus within 1 kb, and a sort-by-base setting at the G12 position; re-loading the session in headless JBrowse must render all three tracks.

建议部分得分

40% three tracks; 25% locus; 25% sort setting; 10% session loads.

R08.06.01.02-T10 Identify the sample with a 3 Mb copy-number loss from segmented coverage tracks

原始指令

In IGV load the four segmented copy-number files in input/cnv/ (sample1–4) with the hg38 genome. Find which sample carries a focal 3 Mb loss on chromosome 10 and report sample ID, approximate boundaries and log2 ratio in output/answer.json.

平台: mac · macOS win · Windows lin · Linux
应用: IGV
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 hover · 悬停与上下文
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 3 / 5

建议验证方式

Sample ID exact; boundaries within 300 kb of gold; log2 ratio within 0.15. Distractor samples carry broad arm-level changes on the same chromosome.

建议部分得分

40% sample; 40% boundaries; 20% log2 ratio.

R08.06.01.02-T11 Compare ChIP-seq signal at a promoter across conditions in the WashU browser

原始指令

In the WashU Epigenome Browser (hg38) load the three bigWigs in input/chip/ as a group with a shared y-axis fixed 0–30, add input/genes.bed, navigate to the MYOD1 promoter, and export a session link to output/session.txt plus a screenshot output/view.png. Report which condition has the highest promoter signal in output/answer.json.

平台: web · 任意系统（网页）
应用: WashU Epigenome Browser
交互表面: brow · 浏览器
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 nav · 平移 / 缩放 / 滚动 drag · 拖放
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 3 / 5

建议验证方式

Session must hold the three tracks with fixed 0–30 scale and the locus; highest-signal condition must equal the gold computed over the promoter interval; screenshot shows three aligned tracks with equal scale (axis labels detected).

建议部分得分

30% tracks with fixed scale; 25% locus; 30% correct condition; 15% screenshot.

R08.06.01.02-T12 Confirm a de novo variant in a trio and report parental allele support

原始指令

In IGV load input/child.bam, father.bam and mother.bam in a multi-locus panel at the candidate variant in input/candidate.txt. Decide whether it is de novo, inherited or an artifact, and report the call with child alt/ref counts and each parent's alt read count in output/answer.json.

平台: mac · macOS win · Windows lin · Linux
应用: IGV
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 click · 指向与点击 hover · 悬停与上下文
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 4 / 5

建议验证方式

Call must equal gold; counts within 10% of samtools mpileup values at that position with the same filters. One parent carries two low-quality alt reads that must not be called inherited. samtools, bcftools and pysam are not installed in the agent image, so allele counts must be read in IGV.

建议部分得分

45% call; 35% child counts; 20% parental counts.

R08.06.01.02-T13 Characterize a complex insertion from soft-clipped reads in IGV

原始指令

In IGV load input/sample.bam at the locus in input/region.txt, show soft-clipped bases, and determine the inserted sequence (≥30 bp) and its exact insertion point from clipped read ends on both sides. Report the insertion point and sequence in output/answer.json.

平台: mac · macOS win · Windows lin · Linux
应用: IGV
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 click · 指向与点击 hover · 悬停与上下文
工作产物: WP12 · 答案 / 决策
条件: long · 长流程
提案难度: 5 / 5

建议验证方式

Insertion point within 5 bp of gold; reported sequence ≥90% identical to gold over ≥30 bp (alignment). Assembly tools, samtools and pysam are not installed and no insertion call is in any VCF, so clipped sequence must be read in IGV.

建议部分得分

35% insertion point; 50% sequence identity; 15% consistent with reads on both sides.

R08.06.01.02-T14 Build a UCSC Track Hub for three bigWigs and load it as a composite

原始指令

Create a UCSC track hub in output/hub/ (hub.txt, genomes.txt, trackDb.txt) serving the three bigWigs in input/bw/ for hg38 as a composite track with subgroups by mark, viewLimits 0:25 and a colour per mark. Serve output/hub/ at http://fixtures.local/hub/ (the harness web server) and load hub.txt in the local UCSC mirror (Genome Browser in a Box), verify it renders at chr1:1,000,000-1,100,000, and save the session link to output/session.txt.

平台: web · 任意系统（网页） lin · Linux
应用: UCSC Genome Browser · Genome Browser in a Box
交互表面: brow · 浏览器 term · 终端
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: type · 文字与表单 click · 指向与点击 code · 代码与命令
工作产物: WP08 · 应用 / 系统状态
条件: tutorial · 阅读文档 / 教程 multiapp · 多应用
提案难度: 4 / 5

建议验证方式

hubCheck passes with no errors; trackDb declares a composite with three subtracks, subgroups, viewLimits 0:25 and distinct colours; the saved session shows the hub loaded and the three subtracks visible at the locus.

建议部分得分

35% valid hub files; 25% composite/subgroups; 20% display settings; 20% loaded session.

R08.06.01.02-T15 Judge four variants in homopolymers and low-complexity regions in IGV

原始指令

In IGV load input/sample.bam and the four indels in input/indels.vcf, all inside homopolymers or short tandem repeats. Using read-level evidence (repeat length distribution, strand pattern, flanking mismatches) label each 'true' or 'artifact' in output/labels.csv with the repeat unit and length you observed.

平台: mac · macOS win · Windows lin · Linux
应用: IGV
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 hover · 悬停与上下文
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 4 / 5

建议验证方式

Labels must match gold (from PCR-free long-read truth) for all four; repeat unit and length must match the reference annotation for each site. No repeat annotation track is provided; samtools, pysam and indel realigners are not installed in the image.

建议部分得分

80% correct labels (20 pts each); 20% repeat annotations correct.

R08.06.01.02-T16 Control: classify the five variants from pileup metrics on the command line

原始指令

Control pair of T01. Using samtools and bcftools from the terminal on input/sample.bam and input/calls.vcf, compute per-site metrics (strand counts, MAPQ, read position, soft clips) and write 'true' or 'artifact' plus the deciding metric for each of the five variants to output/labels.csv.

平台: mac · macOS lin · Linux
应用: samtools · bcftools
交互表面: term · 终端
GUI 需求 · 任务设定: CL · CLI 足够
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 2 / 5

建议验证方式

Same labels as the T01 gold; the deciding metric must match the seeded defect per site. Scored as the CLI control of T01.

建议部分得分

80% correct labels (16 pts each); 20% deciding metrics.

R08.06.01.02-T17 Compare a locus between hg19 and hg38 in IGV and report the coordinate shift

原始指令

In IGV load input/sample_hg19.bam with the hg19 genome and input/sample_hg38.bam with hg38, navigate both to the gene in input/gene.txt, and report the start coordinate of its first exon in each assembly plus the offset in output/answer.json. Note in output/notes.txt whether the region is inverted between assemblies.

平台: mac · macOS win · Windows lin · Linux
应用: IGV
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: nav · 平移 / 缩放 / 滚动 click · 指向与点击 multi · 跨应用
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 3 / 5

建议验证方式

Both coordinates within 10 bp of the gold annotations and the offset consistent; the inversion statement must match the UCSC liftOver chain for that region.

建议部分得分

35% hg19 coordinate; 35% hg38 coordinate; 30% orientation statement.

R08.06.01.02-T18 Review ten candidate somatic variants in a tumour/normal pair and triage them

原始指令

In IGV load input/tumor.bam and input/normal.bam with input/candidates.vcf (10 sites). For each, label 'somatic', 'germline' or 'artifact' from read evidence in both samples, record tumour VAF, and write output/triage.csv. Save a snapshot per site to output/snapshots/ via IGV's snapshot command.

平台: mac · macOS win · Windows lin · Linux
应用: IGV
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 click · 指向与点击 hover · 悬停与上下文
工作产物: WP12 · 答案 / 决策
条件: long · 长流程
提案难度: 4 / 5

建议验证方式

≥9 of 10 labels must match gold; each tumour VAF within 0.05 of the pileup value; 10 snapshots present at the right loci (image centre coordinate recorded in filenames). samtools, pysam and VAF callers are not installed on the VM; snapshots must come from IGV's snapshot command.

建议部分得分

60% labels (6 pts per site); 25% VAFs; 15% snapshots.

R08.06.01.02-T19 Reconcile discordant variant calls from two pipelines in IGV

原始指令

input/pipelineA.vcf and input/pipelineB.vcf disagree at eight sites in input/sample.bam. In IGV review each site and write output/adjudication.csv with the site, which pipeline is right (or 'neither'), and the evidence class (alignment error, left-alignment difference, filter threshold, true miss).

平台: mac · macOS win · Windows lin · Linux
应用: IGV
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 hover · 悬停与上下文 click · 指向与点击
工作产物: WP12 · 答案 / 决策
条件: long · 长流程
提案难度: 5 / 5

建议验证方式

≥7 of 8 adjudications must match gold and the evidence class must match the seeded cause at each site (two are representation-only differences that must be called 'neither'). bcftools, samtools and pysam are not installed in the image, so representation differences must be judged in the viewer.

建议部分得分

55% adjudications; 35% evidence classes; 10% complete file.

R08.06.01.02-T20 Check an exon for off-target CRISPR editing in amplicon reads with IGV

原始指令

In IGV load input/amplicon.bam at the three predicted off-target sites in input/offtargets.bed. Decide for each whether indels at the cut site exceed the background seen in input/control.bam, and report edited yes/no with approximate indel frequency in output/answer.json.

平台: mac · macOS win · Windows lin · Linux
应用: IGV
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: nav · 平移 / 缩放 / 滚动 vis · 视觉判断 hover · 悬停与上下文
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 3 / 5

建议验证方式

Calls must match gold at all three sites; frequencies within 3 percentage points of the pileup values. One site has a 1% sequencing-error background that must be called unedited. CRISPResso, samtools and pysam are not installed in the image.

建议部分得分

75% site calls (25 pts each); 25% frequencies.

已有研究映射

以下沿用研究目录中的基准与小类映射，不是逐题标注、执行记录或产品背书。

Agents' Last Exam (ALE)

基因组浏览器与变异检查

任务提案 · 20

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建议验证方式

建议部分得分

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建议验证方式

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建议验证方式

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原始指令

建议验证方式

建议部分得分

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建议验证方式

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原始指令

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原始指令

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建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

已有研究映射

同工作流族的小类