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
14 months ago by
lffu_003230
lffu_003230 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 • 1.4k views
ADD COMMENTlink modified 14 months ago by WouterDeCoster38k • written 14 months ago by lffu_003230
1

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

ADD REPLYlink modified 14 months ago • written 14 months ago by Devon Ryan89k

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 14 months ago by ATpoint15k

thank you very much.

ADD REPLYlink written 10 months ago by lffu_003230
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