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Samtools bam processor

Skill a5c-ai/babysitter/library/specializations/domains/science/bioinformatics/skills/samtools-bam-processor

BAM/SAM file manipulation skill for sorting, indexing, filtering, and extracting alignment dataFrom its SKILL.md

Install
npx -y skills add a5c-ai/babysitter --skill samtools-bam-processor

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SKILL.md

1.6 KB, 192 tokens by cl100k_base, as published. Nobody here has run it

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)

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

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