Question: [bwa sai2sam_pe] fail to locate the index
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11 months ago by
genomics Newbie20 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, hg19.sa 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 • 826 views
ADD COMMENTlink written 11 months ago by genomics Newbie20

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

ADD REPLYlink written 11 months ago by swbarnes24.8k

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 11 months ago by genomics Newbie20
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