Question: what is the detailed information of .amb .ann .bwt .pac .sa files generated by the BWA aligner?
gravatar for lffu_0032
3 months ago by
lffu_00320 wrote:

i am new to bwa aligner, and i indexed hg19 chr1 using BWA [index] method: bwa index -p hg19.chr1 -a bwtsw /Users/lffu/bio-info/reference/genome/hg19/chr1.fa

after running this command, it generated 5 files: hg19.chr1.amb hg19.chr1.ann hg19.chr1.bwt hg19.chr1.pac

i looked through the bwa official web page and its tutorial, but i did not find more information about the detail meaning of these files, so can anyone help me explain the exact meaning of these 5 files? many thanks here.

.ann bwa alignment .sa .bwt • 279 views
ADD COMMENTlink modified 3 months ago by WouterDeCoster28k • written 3 months ago by lffu_00320

They're internal files needed by BWA, their exact meaning and contents are otherwise irrelevant.

ADD REPLYlink modified 3 months ago • written 3 months ago by Devon Ryan79k

These files represent the burrows-wheeler transformed genome as well as the respective suffix array etc. As Devon said, irrelevant for the end user. If you want details, refer to the BWA paper.

ADD REPLYlink written 3 months ago by ATpoint3.9k
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