alignment-indexing

name	alignment-indexing
description	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.
tool_type	cli
primary_tool	samtools

Version Compatibility

Reference examples tested with: pysam 0.22+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Alignment Indexing

Create indices for random access to alignment files using samtools and pysam.

"Index a BAM file" → Create a .bai/.csi index enabling random access to genomic regions.

• CLI: samtools index file.bam
• Python: pysam.index('file.bam')

Index Types

Index	Extension	Use Case
BAI	.bai	Standard BAM index, chromosomes < 512 Mbp
CSI	.csi	Large chromosomes, custom bin sizes
CRAI	.crai	CRAM index

samtools index

Create BAI Index

samtools index input.bam
# Creates input.bam.bai

Create CSI Index

samtools index -c input.bam
# Creates input.bam.csi

Specify Output Name

samtools index input.bam output.bai

Multi-threaded Indexing

samtools index -@ 4 input.bam

Index CRAM

samtools index input.cram
# Creates input.cram.crai

Index Requirements

Indexing requires coordinate-sorted files:

# Check sort order
samtools view -H input.bam | grep "^@HD"
# Should show SO:coordinate

# Sort if needed, then index
samtools sort -o sorted.bam input.bam
samtools index sorted.bam

Using Indices for Region Access

Goal: Extract reads overlapping specific genomic coordinates from an indexed BAM.

Approach: With the index present, samtools view or pysam.fetch() can jump directly to the relevant file offset instead of scanning the entire file.

samtools view with Region

# Requires index file present
samtools view input.bam chr1:1000000-2000000

Multiple Regions

samtools view input.bam chr1:1000-2000 chr2:3000-4000

Regions from BED File

samtools view -L regions.bed input.bam

pysam Python Alternative

Create Index

import pysam

pysam.index('input.bam')
# Creates input.bam.bai

Create CSI Index

pysam.index('input.bam', 'input.bam.csi', csi=True)

Fetch with Index

with pysam.AlignmentFile('input.bam', 'rb') as bam:
    # fetch() requires index
    for read in bam.fetch('chr1', 1000000, 2000000):
        print(read.query_name)

Check if Indexed

import pysam
from pathlib import Path

def is_indexed(bam_path):
    bam_path = Path(bam_path)
    return (bam_path.with_suffix('.bam.bai').exists() or
            Path(str(bam_path) + '.bai').exists() or
            bam_path.with_suffix('.bam.csi').exists())

if not is_indexed('input.bam'):
    pysam.index('input.bam')

Fetch Multiple Regions

regions = [('chr1', 1000, 2000), ('chr1', 5000, 6000), ('chr2', 1000, 2000)]

with pysam.AlignmentFile('input.bam', 'rb') as bam:
    for chrom, start, end in regions:
        count = sum(1 for _ in bam.fetch(chrom, start, end))
        print(f'{chrom}:{start}-{end}: {count} reads')

Count Reads in Region

with pysam.AlignmentFile('input.bam', 'rb') as bam:
    count = bam.count('chr1', 1000000, 2000000)
    print(f'Reads in region: {count}')

Get Reads Covering Position

with pysam.AlignmentFile('input.bam', 'rb') as bam:
    for read in bam.fetch('chr1', 1000000, 1000001):
        if read.reference_start <= 1000000 < read.reference_end:
            print(f'{read.query_name} covers position 1000000')

Index File Locations

samtools looks for indices in two locations:

input.bam.bai   # Standard location
input.bai       # Alternative location

For CRAM:

input.cram.crai

idxstats - Index Statistics

Get Per-Chromosome Counts

samtools idxstats input.bam

Output format:

chr1    248956422    5000000    0
chr2    242193529    4500000    0
*       0            0          10000

Columns: reference name, length, mapped reads, unmapped reads

Sum Total Mapped Reads

samtools idxstats input.bam | awk '{sum += $3} END {print sum}'

pysam idxstats

with pysam.AlignmentFile('input.bam', 'rb') as bam:
    for stat in bam.get_index_statistics():
        print(f'{stat.contig}: {stat.mapped} mapped, {stat.unmapped} unmapped')

FASTA Index (faidx)

Related but different - index reference FASTA for random access:

samtools faidx reference.fa
# Creates reference.fa.fai

# Fetch region from indexed FASTA
samtools faidx reference.fa chr1:1000-2000

pysam FastaFile

with pysam.FastaFile('reference.fa') as ref:
    seq = ref.fetch('chr1', 1000, 2000)
    print(seq)

Quick Reference

Task	samtools	pysam
Create BAI	samtools index file.bam	pysam.index('file.bam')
Create CSI	samtools index -c file.bam	pysam.index('file.bam', csi=True)
Fetch region	samtools view file.bam chr1:1-1000	bam.fetch('chr1', 0, 1000)
Count in region	samtools view -c file.bam chr1:1-1000	bam.count('chr1', 0, 1000)
Index stats	samtools idxstats file.bam	bam.get_index_statistics()
Index FASTA	samtools faidx ref.fa	Automatic with FastaFile

Common Errors

Error	Cause	Solution
random alignment retrieval only works for indexed BAM	Missing index	Run samtools index file.bam
file is not sorted	Unsorted BAM	Sort first with samtools sort
chromosome not found	Wrong chromosome name	Check names with samtools view -H

Related Skills

• sam-bam-basics - View and convert alignment files
• alignment-sorting - Sort BAM files (required before indexing)
• alignment-filtering - Filter by regions using index
• bam-statistics - Use idxstats for quick counts
• sequence-io/read-sequences - Index FASTA with SeqIO.index_db()