Question: what is the detailed information of .amb .ann .bwt .pac .sa files generated by the BWA aligner?
0
gravatar for lffu_0032
12 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 • 1.1k views
ADD COMMENTlink modified 12 months ago by WouterDeCoster36k • written 12 months ago by lffu_003230
1

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

ADD REPLYlink modified 12 months ago • written 12 months ago by Devon Ryan88k

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 12 months ago by ATpoint13k

thank you very much.

ADD REPLYlink written 8 months ago by lffu_003230
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 751 users visited in the last hour