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  • LAST output as SAM/BAM

    Im testing the sequence read mapping LAST (http://last.cbrc.jp/) But this program only outputs MAF alignment files. I tried using https://github.com/peterjc/maf2sam to convert to SAM/BAM but I get the following error:
    command:
    Code:
    python maf2sam.py reference.fa al.maf
    error:
    Code:
    [maf2sam] Identified 0 read groups
    Traceback (most recent call last):
      File "maf2sam.py", line 514, in <module>
        assert line.startswith("CO\t"), line
    AssertionError: # fraglen=217.0 sdev=146.778 disjoint=0.01 genome=6264404
    Is there another maf to BAM/SAM converter? is there a way to output SAM/BAM from last
    ? Thanks

  • #2
    You may have a look at this log file about how I converted maf to sam.

    Comment


    • #3
      LAST is not outputting MAF in the sense of MIRA Alignment Format (which is what my tool maf2sam.py converts into SAM/BAM).

      Comment

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