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