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FreedomIntelligence/OpenClaw-Medical-SkillsView
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bio-sam-bam-basics
Maintainer FreedomIntelligence · Last updated April 1, 2026
Read, inspect, and manipulate SAM/BAM files with samtools/pysam.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-sam-bam-basics
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- View and convert alignment files using samtools and pysam.
Source Doc
Excerpt From SKILL.md
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
Use cases
- Use bio-sam-bam-basics for genomics and bioinformatics workflows.
- Apply bio-sam-bam-basics to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- 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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