domains / families / science / alignment-indexing

alignment-indexing

separate

Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.

When to use

• Create BAI/CSI indices for BAM/CRAM files
• Enable random access to alignment files
• Fetch specific genomic regions
• Index CRAM files
• Check if alignment files are indexed
• Get per-chromosome counts using idxstats

When not to use

• Indexing VCF/BED files with tabix
• Sorting unsorted alignment files

Skill page

Source