Question: what is the detailed information of .amb .ann .bwt .pac .sa files generated by the BWA aligner?
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gravatar for lffu_0032
2.6 years ago by
lffu_003250
lffu_003250 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 hg19.chr1.sa

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 • 3.9k views
ADD COMMENTlink modified 2.6 years ago by WouterDeCoster44k • written 2.6 years ago by lffu_003250
1

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

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Devon Ryan96k

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 2.6 years ago by ATpoint38k

thank you very much.

ADD REPLYlink written 2.3 years ago by lffu_003250
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