genomics-alignment

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Load when computing alignment QC metrics (mapping rate, MAPQ distribution, insert size, duplicate rate, proper-pair rate) from a SAM or BAM file produced by any short-/long-read aligner (BWA / Bowtie2 / Minimap2). Skip when running the alignment step itself or when only FASTQ-level QC is needed (use `genomics-qc`).

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Source SKILL.md: https://github.com/TianGzlab/OmicsClaw/blob/HEAD/skills/genomics/genomics-alignment/SKILL.md

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genomics-alignment

When to use

The user has a SAM or BAM file from any aligner (BWA-MEM, Bowtie2, Minimap2, etc.) and wants standard alignment QC: mapped-read count, mapping rate, MAPQ distribution, proper-pair rate, duplicate rate. This skill mirrors samtools flagstat + per-MAPQ binning entirely in pure Python (no samtools install needed). It does not perform alignment — feed in an already-aligned .sam / .bam.

For pre-alignment FASTQ QC use genomics-qc. For variant calling on the aligned reads use genomics-variant-calling.

Inputs & Outputs

Input	Format	Required
Aligned reads	`.sam` (SAM v1.6 text — header + records). Binary `.bam` is NOT supported — convert with `samtools view -h aligned.bam > aligned.sam` first.	yes (unless `--demo`)

Output	Path	Notes
Alignment metrics	`tables/alignment_stats.csv`	one-row table — flagstat-style summary
Report	`report.md` + `result.json`	always

Flow

Open the SAM in text mode (genomics_alignment.py:73 → open(sam_path, "r")) or synthesise a demo SAM at output_dir/demo_alignment.sam (genomics_alignment.py:151).
Stream the records, count flags (mapped / proper-pair / dup / supplementary / secondary).
Bin MAPQ; compute insert-size mean / median (paired only).
Write tables/alignment_stats.csv (genomics_alignment.py:279) + report.md + standardised result.json envelope.

Gotchas

--input REQUIRED unless --demo. genomics_alignment.py:267 raises ValueError("--input required when not using --demo"); non-existent paths raise FileNotFoundError at :270. There is no parser.error shortcut — ValueError propagates as a Python traceback, exit code 1.
Text SAM only — binary BAM raises UnicodeDecodeError. genomics_alignment.py:73 calls open(sam_path, "r") (text mode); there is no pysam import or BAM/CRAM decoder anywhere in the script. Convert BAMs upstream with samtools view -h aligned.bam > aligned.sam. The "no pysam dependency" comment at :43 documents this intent.
No subprocess to samtools. Parsing is pure-Python — the script never shells out. CRAM input is not supported either.
No alignment is performed. This skill only summarises an already-aligned file. To produce the SAM/BAM, run BWA / Bowtie2 / Minimap2 yourself first; this skill consumes their output.
Demo writes a synthetic SAM into output_dir. genomics_alignment.py:151 writes demo_alignment.sam directly into the user-specified output directory. If you re-run --demo with different parameters in the same dir, the file is overwritten silently.
Insert-size statistics are paired-only. Single-end alignments still emit a row — but the insert-size columns will be 0 / NaN. Inspect summary['proper_pair_rate'] to confirm the input is paired before drawing conclusions.

Key CLI

# Demo (synthetic 1K-read SAM)
python omicsclaw.py run genomics-alignment --demo --output /tmp/align_demo

# Real BAM
python omicsclaw.py run genomics-alignment \
  --input sample.aligned.bam --output results/

See also

references/parameters.md — every CLI flag
references/methodology.md — flagstat field semantics, MAPQ interpretation
references/output_contract.md — tables/alignment_stats.csv schema
Adjacent skills: genomics-qc (upstream — FASTQ-level QC before alignment), genomics-variant-calling (downstream — variant discovery on the BAM), genomics-cnv-calling (downstream — depth-of-coverage CNV from the BAM)