Index .fasta reference genome

Good day; I am really new at using GATK and all programs suggested by the pipeline. I am currently attempting to initiate alignments with BWA as is required I then proceeded to index the reference human genome.fasta file. When I enter the following command: bwa index -p ucsc.hg19.fasta.bwt -a bwtsw ucsc.hg19.fasta....
I received the following message: [bwa_index] Pack FASTA... [bns_fasta2bntseq] fail to open file 'ucsc.hg19.fasta.bwt.pac'. Abort!...
Could anyone please explain what the 'ucsc.hg19.fasta.bwt.pac' file is and and at which point this must be created. I did not see any references to this is the BWA manual and was hoping that I could find some additional help here.

Thank you in advance.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Juliet,

    BWA is not our tool, so we cannot answer your question. We only answer questions about GATK. Other users in the community may be able to answer you, but you would probably be better off asking this to the people who develop and maintain BWA.

  • KurtKurt Member ✭✭✭

    You are probably confusing the command line. the *pac file is actually a file that will be created by running bwa index (along with a couple of other files that it will create), they are needed for when you actually do the alignments.

    your command line should be

    bwa index -a bwtsw ucsc.hg19.fasta

    Geraldine is right, you should join the BWA forum to ask them questions;

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  • julietjuliet Member

    Thank you for the assistance...

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