Is The Bwa Reference Indexing The Same Thing That Fasta Indexing With Samtools?

Question

[Pablo Marin-Garcia]

I have the human reference indexed with samtools samtools faidx, can I use it with bwa? is this file equivalent to the output of bwa index?

Answer 1

[Pierre Lindenbaum]

A faidx index is just a tiny text file containing:

• the file offset of the sequences in the file
• the length of the sequences
• the names of the sequences
• the length of the Fasta lines

An index for BWA is a much more bigger binary Burrows–Wheeler-compressed index of the sequences prefix one can find in the whole genome.

[Pablo Marin-Garcia]

That is what I thought. So I need to index it with bwa then. Does the 1000 genome project or similar have this data already indexed by bwa? (bwa say that takes 3hours and 2.5 gb). I am using the 1kg reference as suggested here