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  • bwa index error with hg19

    I indexed the ucsc.hg19.fasta for bwa using:

    Code:
    bwa index -p hg19bwaidx -a bwtsw /home/cmccabe/Desktop/NGS/bwa-0.7.12/ucsc.hg19.fasta
    However, I am getting:

    Code:
    cmccabe@DTV-A5211QLM:~/Desktop/NGS$ bwa mem -M -t 16 /home/cmccabe/Desktop/NGS/bwa-0.7.12/ucsc.hg19.fasta /home/cmccabe/IDP/NA12878-NextSeq-S1_R1.fastq.gz /home/cmccabe/IDP/NA12878-NextSeq-S1_R2.fastq.gz > /home/cmccabe/IDP/bwa_reads.sam 
    [B][E::bwa_idx_load_from_disk] fail to locate the index files[/B]
    Why the error? The path to the index files is there. Thank you

    Index files:
    Code:
    hg19bwaidx.ann hg19bwaidx.bwt hg19bwaidx.amb hg19bwaidx.pac hg19bwaidx.sa

  • #2
    bwa indexes are included in the iGenomes bundle in /path_to/Sequence/BWAIndex. You did not need to make your own.

    Since you gave a prefix name for your index try this

    Code:
    $ ~/Desktop/NGS$ bwa mem -M -t 16 /path_to/hg19bwaidx /home/cmccabe/IDP/NA12878-NextSeq-S1_R1.fastq.gz /home/cmccabe/IDP/NA12878-NextSeq-S1_R2.fastq.gz > /home/cmccabe/IDP/bwa_reads.sam

    Comment

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