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  • extended cigar in bwa-mem

    Hi all,

    I am aligning pacbio reads to a reference genome using bwa mem. Do you know how to output an extended CIGAR in output sam file from bwa v0.7.13?

    My command is:
    Code:
    bwa mem -x pacbio refgenome.fasta reads.fastq > output.sam
    Thanks in advance

  • #2
    What exactly do you mean by "extended CIGAR"? bwa mem will output SAM files with an appropriate CIGAR string already.

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    • #3
      He probably means cigar strings with X and = symbols instead of M, which are very handy.

      Comment


      • #4
        Yes, this is what I mean by "extended cigar". By the way, I found a tool that can do that a posteriori, in case someone else is interested: SamFixCigar (http://github.com/lindenb/jvarkit )

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        • #5
          Are there any plans to extend bwa to write X/= instead of M? At least optional?

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          • #6
            You can now use BBMap's reformat.sh to add those:

            reformat.sh in=mapped.sam out=extended.sam sam=1.4

            I have not tested it extensively on things like hard-clipping but it should generally work.

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            • #7
              Brian,

              thanks for the suggestion. I will try :-)

              Nevertheless I'd wish bwa would provide an option to either use M or X=.
              Just to avoid more I/O due to another conversion ...

              Sven

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              • #8
                After studying some docs I do see that with optional MD:Z I am even as flexible as with X=, with the advantage of not having too "complicated" CIGARs. :-)

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