Can You Please Tell Me Where I Find Information About .Fai File Format?

Question

[Biomed]

I am playing with GATK but the web site states fai as the ref file format however I have access to reference alignments as maf files. Can you help me with this?

Answer 1

[Madelaine Gogol]

Purely for my future self if I google this again, the columns of a .fai file appear to be:

• chromosome name
• chromosome length
• offset of the first base of the chromosome sequence in the file
• length of the fasta lines
• some other length of the fasta lines called "line_blen" in the source code? Appears to typically (for me) be length of fasta line + 1.

ETA: Oh, Pierre already answered this over here. blen is number of bytes in each fasta line.

Answer 2

[brentp]

that is an index of your fasta file. have a look at samtools:

Once installed, you can create an index of some.fasta as

samtools faidx some.fasta

this will create some.fasta.fai

and have a look here where it describes how to set up your data for GATK.

[mylons]

Is there a way to do this with picard or GATK itself? I'd love to stay away from samtools if I could.

Answer 3

[Pierre Lindenbaum]

The FAIDX file is created by samtools faidx. The FAIDX file contains, among other things, the

• name of the reference sequence (chr1, chr2...)
• the offset of the first base of this sequence in the file
• the length of the FASTA lines

with this information, samtools can quickly access any region of the genome.

See also this post I wrote about faidx

[Paul]

Dear Pierre,

So if I understand right - if I need bed file from my fa.fai I can do just

awk 'OFS="\t" {print $1,$3,$2}' in.fai

? Thank you so much.

Answer 4

[John Marshall]

HTSlib has provided a manual page describing this format for a few years now. See man 5 faidx, also on the web at faidx(5) manual page.