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BI
bio-alignment-filtering
Maintainer FreedomIntelligence · Last updated April 1, 2026
Filter alignments by flag, quality, region, or paired status.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-alignment-filtering
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Filter alignments by flags, quality, and regions using samtools and pysam.
- samtools view -F 3332 -q 30 -o filtered.bam input.bam.
Source Doc
Excerpt From SKILL.md
Filter Flags
| Option | Description |
|---|---|
-f FLAG | Include reads with ALL bits set |
-F FLAG | Exclude reads with ANY bits set |
-G FLAG | Exclude reads with ALL bits set |
-q MAPQ | Minimum mapping quality |
-L BED | Include reads overlapping regions |
Common FLAG Values
| Flag | Hex | Meaning |
|---|---|---|
| 1 | 0x1 | Paired |
| 2 | 0x2 | Proper pair |
| 4 | 0x4 | Unmapped |
| 8 | 0x8 | Mate unmapped |
| 16 | 0x10 | Reverse strand |
| 32 | 0x20 | Mate reverse strand |
| 64 | 0x40 | First in pair (read1) |
| 128 | 0x80 | Second in pair (read2) |
| 256 | 0x100 | Secondary alignment |
| 512 | 0x200 | Failed QC |
| 1024 | 0x400 | Duplicate |
| 2048 | 0x800 | Supplementary |
Keep Only Primary Alignments
samtools view -F 256 -F 2048 -o primary.bam input.bam
Use cases
- Use bio-alignment-filtering for genomics and bioinformatics workflows.
- Apply bio-alignment-filtering 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
- sam-bam-basics - View and understand alignment files
- alignment-sorting - Sort before/after filtering
- alignment-indexing - Required for region filtering
- duplicate-handling - Mark duplicates before filtering
- bam-statistics - Check filter effects
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