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数据与复现
BI
bio-sam-bam-basics
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Read, inspect, and manipulate SAM/BAM files with samtools/pysam.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-sam-bam-basics
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- View 、 convert alignment files ，使用 samtools 、 pysam。
原始文档
SKILL.md 摘录
SAM Format Structure
Header lines start with @:
@HD- Header metadata (version, sort order)@SQ- Reference sequence dictionary@RG- Read group information@PG- Program used to create file
Alignment fields (tab-separated):
- QNAME - Read name
- FLAG - Bitwise flag
- RNAME - Reference name
- POS - 1-based position
- MAPQ - Mapping quality
- CIGAR - Alignment description
- RNEXT - Mate reference
- PNEXT - Mate position
- TLEN - Template length
- SEQ - Read sequence
- QUAL - Base qualities
- Optional tags (NM:i:0, MD:Z:50, etc.)
Common Flags
| Flag | Decimal | Meaning |
|---|---|---|
| 0x1 | 1 | Paired |
| 0x2 | 2 | Proper pair |
| 0x4 | 4 | Unmapped |
| 0x8 | 8 | Mate unmapped |
| 0x10 | 16 | Reverse strand |
| 0x20 | 32 | Mate reverse strand |
| 0x40 | 64 | First in pair |
| 0x80 | 128 | Second in pair |
| 0x100 | 256 | Secondary alignment |
| 0x200 | 512 | Failed QC |
| 0x400 | 1024 | PCR duplicate |
| 0x800 | 2048 | Supplementary |
CIGAR Operations
| Op | Description |
|---|---|
| M | Alignment match (can be mismatch) |
| I | Insertion to reference |
| D | Deletion from reference |
| N | Skipped region (introns in RNA-seq) |
| S | Soft clipping |
| H | Hard clipping |
| = | Sequence match |
| X | Sequence mismatch |
Example: 50M2I30M = 50 bases match, 2 base insertion, 30 bases match
适用场景
- Use bio-sam-bam-basics ，用于 genomics 、 bioinformatics workflows。
- Apply bio-sam-bam-basics to sequencing，variant，或 omics analysis tasks。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- alignment-indexing - Create indices for random access (required for fetch/region queries)
- alignment-sorting - Sort alignments by coordinate or name
- alignment-filtering - Filter alignments by flags, quality, regions
- bam-statistics - Generate statistics from alignment files
- sequence-io/read-sequences - Parse FASTA/FASTQ input files
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