Samtools faidx

samtools faidx creates an index for a FASTA file and enables random-access extraction of subsequences by coordinate. The index is required by many downstream tools (GATK, BWA, bcftools) before they can process a reference genome.

Details

Property	Value
Type	Native tool
Binary	samtools
Subcommand	faidx

Installation

Samtools must be installed and available in your system PATH.

macOS (Homebrew)

brew install samtools

Ubuntu/Debian

sudo apt install samtools

conda

conda install -c bioconda samtools

Accepted inputs

Extension	Description
.fasta, .fa, .fna	Uncompressed FASTA (required for indexing)
.fasta.gz, .fa.gz	Bgzip-compressed FASTA (requires bgzip, not regular gzip)

gzip vs bgzip

samtools faidx can only index FASTA files compressed with bgzip, not regular gzip. A bgzip-compressed file has the same .gz extension but a different internal format. If indexing fails on a .gz file, decompress it with gunzip and re-index the uncompressed version.

Usage

Create index

1. Navigate to Tools → Samtools faidx.
2. Select a FASTA file from your Data library.
3. Click Create index.

Liatir runs samtools faidx <file>, which creates <file>.fai in the same directory. The index file is automatically registered in the Data library.

The results panel shows a table of all sequences in the FASTA with their lengths.

Extract subsequence

With a file selected and an existing .fai index, use the Extract subsequence form:

1. Enter a region string in the format chr:start-end (1-based, inclusive).
2. Click Extract.

The extracted FASTA sequence is displayed inline. Examples:

Region string	Extracts
chr1	Entire chromosome 1
chr1:1-1000	First 1000 bases of chr1
chr17:7,668,421-7,687,538	TP53 locus

The .fai index format

The .fai file is a tab-separated text file with one line per sequence:

NAME    LENGTH    OFFSET    BASES_PER_LINE    BYTES_PER_LINE
chr1    248956422    52    60    61
chr2    242193529    253404903    60    61

Column	Description
NAME	Sequence name from the > header (up to first whitespace)
LENGTH	Sequence length in bases
OFFSET	Byte offset of the first base in the FASTA file
BASES_PER_LINE	Number of bases per line
BYTES_PER_LINE	Bytes per line (includes newline)

The index allows tools to jump directly to any position in the file without reading from the start.