samtools-bam-processor
BAM/SAM file manipulation skill for sorting, indexing, filtering, and extracting alignment data
Profile →npx skills add a5c-ai/babysitter --skill samtools-bam-processor --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Samtools BAM Processor Skill ## Purpose Provide BAM/SAM file manipulation capabilities for sorting, indexing, filtering, and extracting alignment data. ## Capabilities - BAM sorting and indexing - Duplicate marking and removal - Alignment statistics generation - Region extraction and filtering - Read group management - Format conversion (SAM/BAM/CRAM) ## Usage Guidelines - Sort and index BAM files for efficient access - Mark or remove duplicates based on protocol - Generate alignment statistics for quality assessment - Extract regions of interest for targeted analysis - Manage read groups for multi-sample data - Use CRAM for storage efficiency ## Dependencies - samtools - Picard - sambamba ## Process Integration - Whole Genome Sequencing Pipeline (wgs-analysis-pipeline) - Tumor Molecular Profiling (tumor-molecular-profiling) - RNA-seq Differential Expression Analysis (rnaseq-differential-expression)
- Purpose
- Capabilities
- Usage Guidelines
- Dependencies
- Process Integration
What does the samtools-bam-processor skill do?
BAM/SAM file manipulation skill for sorting, indexing, filtering, and extracting alignment data
How do I install it?
Run `npx skills add a5c-ai/babysitter --skill samtools-bam-processor --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From a5c-ai/babysitter, a repository with 1,642 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.