samtools-bam-processing

What problem does it solve?

This Skill provides a robust command-line toolkit for manipulating SAM, BAM, and CRAM alignment files, essential for next-generation sequencing (NGS) data analysis.

Core Features & Use Cases

• Format Conversion: Convert between SAM, BAM, and CRAM formats to optimize storage and compatibility.
• Sorting and Indexing: Sort BAM files by coordinate or read name and create indexes for efficient random access.
• Quality Control: Generate crucial statistics like mapping rates, insert sizes, and coverage depth.
• Filtering and Deduplication: Filter reads based on mapping quality or FLAG bits, and mark or remove PCR duplicates.
• Use Case: After aligning sequencing reads, use this Skill to sort, index, and generate quality control reports for your BAM files, preparing them for downstream variant calling or analysis.

Quick Start

Use the samtools skill to sort the input.bam file by coordinate and then index the sorted file.