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  • jorge
    Member
    • Jun 2011
    • 25
    #1

    unexpected BWA output when enabling multihit

    Hello,

    I have aligned with BWA and allowed a maximum of 100 multiple hits with this command:
    bwa samse -n 100 database.fasta aln_sa.sai short_read.fastq > aln.sam

    However the output file is not a sam file (see below) which I expected. Has anybody experience the same?

    Thanks
    Jorge

    >SRR030012.5 100 30957
    chr10 -126484170 0
    chr3 -1113010 0
    chr2 -232514635 0
    chr16 -6430412 0
    chr3 -115750401 0
    chr8 -26092084 0
    chr5 -89789506 0
    chr1 -179320160 0
    chr4 -80353991 0
    chr1 -169779976 0
    chr2 -57672668 0
    chr6 -126943760 0
    chr2 -115944596 0
    chr16 -58665846 0
    chr12 -77323712 0
    chr12 -8541015 0
    chr12 -75575699 0
    chr3 -90117294 0
    chr8 -20402676 0
    chr15 -60835375 0
    chr2 -231853752 0
    chr2 -218080361 0
    chr8 -137370420 0
    chr21 -22766790 0
    chr8 -112168254 0
    chr4 -36842765 0
    chr2 -79057663 0
    chr2 -143434625 0
    chrY -25246452 0
    chr10 -1535935 0
    chr2 -91704688 0
    chr12 -112848359 0
    chr3 -107334853 0
    chr8 -111667999 0
    Tags: None
  • jorge
    Member
    • Jun 2011
    • 25
    #2
    Hi,

    I found out I was using an old version of BWA, moving to the latest version gave me the expected sam file.

    Jorge

    Comment

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