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SophiaSophia Member
edited July 2012 in Ask the GATK team

Dear all,

I was browsing through some of the less used functions in the GATK documentation, hence the following question:
Does the LeftAlignIndels function do something additional that is not happening with IndelRealigner? In other words, do you recommend to run LeftAlignIndels on top of the indel realignment?

Best regards,


  • ebanksebanks Broad InstituteMember, Broadie, Dev

    No, it's only necessary if you are dealing with tools downstream that don't do haplotype resolution on their own. For example, I wrote this tool so that IGV screenshots would look better by making the indels consistently aligned.

  • SophiaSophia Member

    I see, good to know, thanks.

  • Dear All,
    You mention the 'convention to leftalign indels' in the description of the tool. I have been looking for any 'officially' looking documentation of such a convention and haven't found any. Can anyone by any chance point me towards somewhere where this convention is documented or described?
    Best regards,

  • Hi Anne-Mette,

    good question, I am in fact wondering about the same thing. The only convention/recommendation I could find, virtually states the entire opposite, i.e. that indels shall be right-aligned (see:

    The whole left/right-alignment thing obviously becomes important, when you start to compare variants of different sources, e.g. variation calls of any custom-pipeline to annotated variants that have originally been called differently.

    Thanks in advance,

  • ebanksebanks Broad InstituteMember, Broadie, Dev

    The left-alignment is described in the VCF specification itself.

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