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LeftAlignIndels

SophiaSophia Member Posts: 50
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,
Sophia

Answers

  • ebanksebanks Broad InstituteMember, Administrator, Broadie, Moderator, Dev Posts: 698 admin

    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.

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

  • SophiaSophia Member Posts: 50

    I see, good to know, thanks.

  • amheinamhein Member Posts: 1

    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,
    Anne-Mette

  • AppeltJUAppeltJU Member Posts: 1

    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: http://www.hgvs.org/mutnomen/recs-DNA.html#del).

    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,
    Uwe

  • ebanksebanks Broad InstituteMember, Administrator, Broadie, Moderator, Dev Posts: 698 admin

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

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

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