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  • Crossbow alignment format

    I am using crossbow v1.1.1 on a local computer cluster to map a set of human SOLiD reads and call the variants. Crossbow glues together the bowtie aligner and SOAPsnp variant caller, and does this in a highly parallel fashion with an option to use the Amazon cloud.

    Currently, the program works well and the final SNP output is what is expected. However, I also need the alignment information from the initial bowtie alignment in BAM format, which crossbow does not currently support. Crossbow alignment output files can be retained and are in a 10-column tab-delimited format, but the format does not match standard bowtie output or SOAPsnp input. The following are four lines from the crossbow alignment file:

    19 0061 061971493 + TGAGTGAATTACATCATATCCACACAGATGAATGTATTACATCATATC `aXXc__^^_NR^[_`ac_^^ZMLZRTVSOLU?!<S8!+O?!6WS@1- 0 34:A>T 0 r
    16 0005 005054723 - GCATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGTGTGTGTGAG !!!!GHEFOM>17?ILDDB?BLUA579JRC3:G@JYYJLa_^__TQ]` 0 - 0 r
    2 0051 051640947 - TTGGCATCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGTGCCTGG '/5L^;<]PE@@7AFDX][VZ^^ac`[UYbVV``ZZb`_ab_Y\__ba 0 - 0 r
    19 0055 055523009 + GTGAGCCGAGATCGCACCACTGCACTCCAGCCTGGGCGACAGAGTGAG ccccccccccbb_XZ]YUYab``ba[]aVTY[]QU_XZIBXacYW`aA 91 - 0 r


    Some of these columns are obvious and others are not (at least to me). From what I can gather the fields are:
    1: chromosome ID
    2: ??
    3: start position in reference
    4: strand orientation
    5: read bases
    6: quality string
    7: ??
    8: variant call (0-based)
    9: ??
    10: ?? It's always "r" ??

    My goal is write a script to turn this file into a SAM file and then use SAMtools for other analyses. Any help on this would be greatly appreciated. Thanks.

  • #2
    Hello,

    Did you get a solution to this? I am wondering the same thing. Trying to analyze Crossbow alignment output.

    Thanks

    Comment

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