Does it support structured data output?

Yes, it can export analysis data as JSON, making it easy to integrate results into other applications or data science pipelines.

What programming language is required for the toolkit?

The toolkit uses Python scripts and requires the pysam and typer libraries to be installed in your local environment.

Can I filter reads by mapping quality?

Absolutely. You can apply filters for minimum mapping quality (MAPQ), base quality, proper pairs, and exclude duplicate reads.

Do I need a BAM index file to use this?

Yes, for efficient random access to specific genomic regions, your BAM files should be indexed (typically using 'samtools index') before running the scripts.

Can this skill process CRAM files?

Yes, the BAM Toolkit supports BAM, SAM, and CRAM alignment formats for comprehensive genomic analysis.

BAM Alignment Toolkit

Name: BAM Alignment Toolkit
Author: dakesan

bydakesan

0•

Data Science & ML

Analyzes genomic alignment files to extract reads, identify insertions and deletions, and calculate coverage statistics for WGS and WES data.

The BAM Toolkit provides a specialized set of utilities for bioinformaticians and researchers to interact with BAM, SAM, and CRAM alignment files within Claude. It streamlines sequence analysis workflows by enabling high-precision read extraction, CIGAR-based indel identification, and detailed coverage calculation, exporting results in structured JSON or standard BAM formats. This tool is essential for quality control in Whole Genome Sequencing (WGS) or Whole Exome Sequencing (WES) projects, offering deep insights into genomic regions of interest directly through AI-driven commands.

Key Features

010 GitHub stars

02Identify insertions and deletions (indels) with automated CIGAR string parsing

03Structured JSON output for seamless integration with downstream data analysis

04Calculate comprehensive coverage statistics including mean, median, and percent covered

05Extract reads from specific genomic regions as JSON or BAM formats

06Apply advanced filtering for mapping quality, base quality, and proper pairs

Use Cases

01Exporting read data to JSON for custom visualization or integration into data science pipelines

02Validating variant calls by extracting and grouping high-quality supporting reads for indels

03Performing quality control and coverage assessment for specific target regions in WES data

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add dakesan/cc-dnawork-plugin bam-toolkit

For use in Claude.ai and ChatGPT

Download Skill