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sam-bam-basics

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View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.

When to use

• inspecting alignments
• converting between formats
• understanding alignment file structure
• viewing BAM as SAM
• viewing specific regions
• counting alignments
• decoding flags
• format conversion

Skill page

Source