Samtools FAQs

Question 1

What file formats does Samtools MCP support?

Accepted Answer

Samtools MCP natively supports SAM (text), BAM (binary), and CRAM (compressed) alignment file formats, allowing for seamless conversion between them.

Question 2

How can I install and use Samtools MCP?

Accepted Answer

The easiest way to use Samtools MCP is through Docker. Alternatively, you can install it locally by cloning the repository and installing the required dependencies using pip. Configuration details for both methods are available in the documentation.

Question 3

Can I analyze specific genomic regions with Samtools MCP?

Accepted Answer

Yes, Samtools MCP allows you to extract and analyze specific genomic regions within your alignment files using features like region filtering and depth calculation.

Question 4

What are some common use cases for Samtools MCP?

Accepted Answer

Common use cases include viewing and converting alignment files, sorting reads, indexing BAM/CRAM files for faster access, generating alignment statistics, and filtering reads based on specific criteria.

Question 5

What is Samtools MCP?

Accepted Answer

Samtools MCP (Model Control Protocol) provides a standardized interface for working with SAM, BAM, and CRAM alignment files, simplifying common tasks like viewing, sorting, and indexing.

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