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bio-alignment-indexing

separate

Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam to enable random access or fetch specific genomic regions.

When to use

• Create BAI index
• Create CSI index
• Index CRAM files
• Fetch specific genomic regions
• Count reads in region
• Get index statistics
• Index reference FASTA

When not to use

• Sort BAM files
• Filter by regions
• View and convert alignment files

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Source