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

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?

next-gen sequencing bwa fasta
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Pablo Marin-Garcia Pablo Marin-Garcia

1 answer

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.

• 2 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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

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updated by Ram Ram • written by Pablo Marin-Garcia Pablo Marin-Garcia

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