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Babysitter samtools-bam-processor

BAM/SAM file manipulation skill for sorting, indexing, filtering, and extracting alignment data

install
source · Clone the upstream repo
git clone https://github.com/a5c-ai/babysitter
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/a5c-ai/babysitter "$T" && mkdir -p ~/.claude/skills && cp -r "$T/library/specializations/domains/science/bioinformatics/skills/samtools-bam-processor" ~/.claude/skills/a5c-ai-babysitter-samtools-bam-processor && rm -rf "$T"
manifest: library/specializations/domains/science/bioinformatics/skills/samtools-bam-processor/SKILL.md
tags
#bam-processing#sam-manipulation#alignment-analysis#sequence-tools#bioinformatics
source content

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)