bio-mcp/bio-mcp-samtools

3.2

If you are the rightful owner of bio-mcp-samtools and would like to certify it and/or have it hosted online, please leave a comment on the right or send an email to henry@mcphub.com.

MCP server for Samtools, a suite of utilities for interacting with high-throughput sequencing data in SAM, BAM, and CRAM formats.

Tools

Functions exposed to the LLM to take actions

samtools_view

View and convert alignment files, with options for filtering by region, flags, and quality.

samtools_sort

Sort SAM/BAM files by coordinate or read name.

samtools_index

Create an index for sorted BAM/CRAM files.

samtools_stats

Generate detailed statistics from an alignment file.

samtools_flagstat

Count reads in each FLAG category, providing a quick summary of alignment status.

samtools_depth

Calculate the per-position read depth across a specified region or the entire file.