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Old 03-10-2012, 03:10 PM   #1
Location: Vermont

Join Date: Mar 2012
Posts: 12
Default BWA not creating rBWT file

Hi everyone,

I have BWA version 0.6.1 and for some reason it is not creating the .rbwt file in the human genome:

bash-3.2$ ~/MPS/programs/bwa-0.6.1/bwa index -a bwtsw genome.fa


-rwxr-xr-x 1 rbarrant usr 3142044949 Mar 10 14:45 genome.fa
-rw-r--r-- 1 rbarrant usr 6144 Mar 10 16:26 genome.fa.amb
-rw-r--r-- 1 rbarrant usr 941 Mar 10 16:26 genome.fa.ann
-rw-r--r-- 1 rbarrant usr 3080436148 Mar 10 16:25 genome.fa.bwt
-rw-r--r-- 1 rbarrant usr 770109014 Mar 10 16:26 genome.fa.pac
-rw-r--r-- 1 rbarrant usr 1540218080 Mar 10 17:01

any suggestions?

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Old 03-10-2012, 04:49 PM   #2
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285

See the "NEWS" file that comes with BWA:

...the index data structure has been changed to support genomes longer than 4GB...
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Old 03-23-2012, 03:27 AM   #3
Location: brussels

Join Date: Mar 2012
Posts: 13

I ramiro2k,
I do have the same problem. In fact I don't care if there is or not rbwt file. the only problem is that without it seems I can't really continue with the gatk pipeline. Did you find something.

did I miss something?
aituka is offline   Reply With Quote

bwa rbwt

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