Question: [bwa sai2sam_pe] fail to locate the index
gravatar for genomics Newbie
3 months ago by
genomics Newbie0 wrote:

I researched my two index error messages (1. [bwa_aln] fail to locate the index 2. [bwa sai2sam_pe] fail to locate the index) and am providing the following details for troubleshooting: : • Used the bwa indexing command…’bwa index -a bwtsw hg.fa -p hg’ o The indexes of hg19.amb, hg19.ann, hg19.bwt, hg19.pac, were successfully created o The above command did not create a bwa sai2sam_pe index. I also checked for this index in samtools.
o Can I download pre-created index files along with the hg19 exome reference?

• BWA version requirement: BWA v0.7.8-r455 o The software package which I am trying to run requires this -r455 bwa revision, but I could not find this version to install so I used the BWA v0.7.8 o I could only locate and download bwa v0.7.8, and not the r455 ?revision.
o Question: Anybody know where I could retrieve this bwa version?

• Does this 0.7.8 version handle paired end reads? o I believe subsequent versions handle paired-end reads, but am thinking the -r455 version may not? o Do I need to specify in my index command that I want indexes to be created for paired end reads?

index bwa • 214 views
ADD COMMENTlink written 3 months ago by genomics Newbie0

Are you sure you have the path to your index correct?

ADD REPLYlink written 3 months ago by swbarnes23.6k

Yes, I believe the path to the index is correct. The path points directly to the location where the hg19.amb, hg19.ann, etc. files are located.

ADD REPLYlink written 3 months ago by genomics Newbie0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1379 users visited in the last hour