TAFFISH REPORT

bam-qc-flow

Project-level BAM quality-control report for aligned sequencing data.面向已比对测序数据的项目级 BAM 质量控制报告。

Flow0.2.0-r1

TAFFISH flow

Generated2026-06-13T14:35:54Z

UTC

Templateflow-report 0.1.0

standalone HTML

Executive summary执行摘要

BAM QC Readiness DashboardBAM 质控就绪状态

Use this section first to confirm how many BAMs were checked, whether target-region coverage was requested, and whether the native MultiQC evidence is available inside this single report.先看这里可快速确认检查了多少 BAM、是否请求目标区域覆盖度，以及原生 MultiQC 证据是否已经内嵌在单文件报告中。

Samples1

validated BAM sample rows已验证 BAM 样本行

Quickcheck1 / 1

samples passed integrity check通过完整性检查的样本

Regionsenabled

mosdepth interval modemosdepth 区间模式

Advanced args2

@step argument blocks used使用的 @step 参数块

Input validationok

Sample table, BAM files, and indexes are readable.样本表、BAM 文件和索引均可读取。

Samtools integrityok

1 of 1 samples passed samtools quickcheck.1/1 个样本通过 samtools quickcheck。

Alignment metricsok

Samtools flagstat, stats, idxstats, and coverage completed for every sample.所有样本完成 Samtools flagstat、stats、idxstats 和 coverage。

Coverage metricsok

mosdepth genome and region summaries were generated.已生成 mosdepth 全基因组与区域覆盖度汇总。

Native reportok

MultiQC report was generated and embedded as a standalone subreport payload.MultiQC 报告已生成，并作为单文件子报告 payload 内嵌。

Standalone reportok

TAFFISH template-compatible BAM QC report was generated.已生成兼容 TAFFISH 模板的 BAM QC 报告。

Workflow logic流程逻辑

From aligned BAM to reviewable QC evidence从已比对 BAM 到可审阅质控证据

This flow does not realign, sort, index, mark duplicates, or call variants. It assumes BAMs are already coordinate-sorted and indexed, then focuses on integrity, mapping statistics, contig distribution, coverage, and report packaging.本流程不重新比对、排序、建索引、标记重复或变异检测；它假定 BAM 已经按坐标排序并建好索引，然后专注于完整性、比对统计、染色体分布、覆盖度和报告封装。

InputBAM + index

→

Samtoolsquickcheck / flagstat / stats / idxstats / coverage

→

mosdepthgenome and optional regions

→

ReportMultiQC + TAFFISH standalone HTML

Embedded subreports内嵌子报告

Native QC Reports原生 QC 报告

Buttons open original program-generated HTML reports as separate local pages from payloads stored inside this single file. The original files also remain in the output tree for audit.按钮会从当前单个 HTML 文件内保存的 payload 打开原始程序生成的 HTML 报告，并作为独立本地页面显示；原始文件也保留在输出目录中用于审计。

MultiQC

MultiQC BAM QC report

04_reports/multiqc_report.html

Original program-generated HTML is stored inside this single report and opens as a separate local page.原始程序生成的 HTML 已保存在这个单文件报告中，并会作为独立本地页面打开。

Open native report打开原生报告

Quality gates质量门控

What passed, what was skipped, and what to inspect next通过、跳过与后续审阅重点

Gate	Status	Evidence	Recommended action
BAM readability	ok	All declared BAM and index files were readable.所有声明的 BAM 与索引文件均可读取。	Proceed to alignment QC review.继续审阅比对质控结果。
BAM integrity	ok	1/1 samples passed samtools quickcheck.1/1 个样本通过 samtools quickcheck。	Investigate any failed samples before downstream analysis.若有失败样本，应先排查再继续下游分析。
Alignment statistics	ok	Samtools metrics are available under 03_results/samtools/.Samtools 指标位于 03_results/samtools/。	Review mapping, proper-pair, duplicate, and supplementary/secondary signals in MultiQC.在 MultiQC 中审阅比对率、proper pair、重复、supplementary/secondary 等信号。
Target coverage	ok	Region coverage and threshold files are available.区域覆盖度与阈值文件已生成。	Use the region summaries to check capture/panel uniformity.用区域汇总检查捕获/面板覆盖均一性。
Report packaging	ok	Main HTML embeds the native MultiQC payload and key tables.主 HTML 内嵌原生 MultiQC payload 和关键表格。	Share bam_qc_report.html for offline review; keep the output tree for audit.离线审阅可分享 bam_qc_report.html；审计请保留完整输出目录。

Sample table样本表

Per-sample primary outputs逐样本主要输出

This table points to the main Samtools and mosdepth outputs for each sample. Paths remain relative to the output directory in the full manifest and file indexes.该表指向每个样本的主要 Samtools 和 mosdepth 输出；完整 manifest 和文件索引中保留相对于输出目录的路径。

Sample	Quickcheck	Flagstat	Stats	Coverage	mosdepth genome
tiny	example-out/03_results/samtools/quickcheck/tiny.quickcheck.txt	example-out/03_results/samtools/flagstat/tiny.flagstat.txt	example-out/03_results/samtools/stats/tiny.stats.txt	example-out/03_results/samtools/coverage/tiny.coverage.tsv	example-out/03_results/mosdepth/genome/tiny.genome.mosdepth.summary.txt

Deliverables交付文件

Files to open first and files for audit优先查看与审计复现文件

Read firstStandalone report

04_reports/bam_qc_report.html

Native QCMultiQC report

04_reports/multiqc_report.html

ReuseSamtools results

03_results/samtools

Reusemosdepth results

03_results/mosdepth

AuditCommands

04_reports/commands.sh

AuditManifest

run.manifest.json

Methods方法说明

How the evidence was produced证据如何生成

Method	Description
Input normalization	BAM and index inputs are validated and linked into 02_intermediate/bam_links so tools can see adjacent indexes without modifying source data.流程验证 BAM 与索引，并在 02_intermediate/bam_links 中创建链接，让工具看到相邻索引而不修改原始数据。
Samtools QC	Samtools quickcheck, flagstat, stats, idxstats, and coverage provide integrity, alignment, contig, and summary coverage metrics.Samtools quickcheck、flagstat、stats、idxstats 和 coverage 提供完整性、比对、染色体和覆盖度摘要指标。
mosdepth QC	mosdepth -n generates compact genome-level coverage summaries, and optional --regions-bed enables interval-level and threshold summaries.mosdepth -n 生成紧凑的全基因组覆盖度摘要；可选 --regions-bed 生成区间级和阈值摘要。
Report aggregation	MultiQC collects native tool outputs; bam_qc_report.html wraps core evidence and embeds the native MultiQC HTML as a same-file subreport.MultiQC 汇总原生工具输出；bam_qc_report.html 包装核心证据，并以内嵌同文件子报告形式包含原生 MultiQC HTML。

Term	Meaning
BAM	Binary Alignment/Map file containing aligned sequencing reads.保存已比对 reads 的二进制 Alignment/Map 文件。
BAI/CSI	Index file required for efficient random access into a BAM.用于 BAM 随机访问的索引文件。
flagstat	Samtools summary of read categories such as mapped, paired, duplicate, secondary, and supplementary reads.Samtools 对 mapped、paired、duplicate、secondary、supplementary 等 reads 类别的摘要。
mosdepth	A fast depth-of-coverage tool used here for compact genome and optional region summaries.快速覆盖深度工具；本流程用于生成紧凑的全基因组和可选区域摘要。
MultiQC	A report aggregator that parses many bioinformatics tool outputs into a single native HTML report.汇总多种生信工具输出并生成原生 HTML 报告的工具。

Provenance溯源

Reproducibility files可复现性文件

The standalone HTML is meant for review and sharing. Keep the full output directory when exact commands, versions, logs, and raw tool outputs are needed.单文件 HTML 适合审阅和分享；如果需要精确命令、版本、日志和原始工具输出，请保留完整输出目录。

File	Role
run.manifest.json	run manifest
04_reports/report.manifest.json	report manifest
04_reports/embedded_html_reports.tsv	embedded HTML payload index
04_reports/versions.tsv	version pins
04_reports/methods.txt	methods text