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Is it useful to call LeftAlignIndels after IndelRealigner

ambi1999ambi1999 United KingdomMember


In my pipeline to find variants in bacterial genome, I am first calling IndelRealigner and then calling variants using HaplotypeCaller. As left aligning of indels seems to be an important step, should I need to call LeftAlignIndels after the IndelRealigner?

I understand that documentation for LeftAlignIndels mentions that it is not required if using sophisticated tools like HaplotypeCaller, but I may be calling variants using other tools such as FreeBayes (just to compare variants found using different tools).

Thanks for reading and any help.



  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi Ambi,

    Both Indel Realignment and Left Alignment are not necessary if you are using HaplotypeCaller.

    For use with other tools that do not do the local reassembly, it may be worth using them. I honestly don't have any experience with this. You can try with and without the tools and compare the results. Also, this answer and this thread may help.


  • ambi1999ambi1999 United KingdomMember

    Hi Shiela,

    Thx. At the moment I am calling IndelRealigner but not LeftAlignIndels.

    Earlier I was thinking that calling IndelRealigner

    Earlier I was thinking that perhaps IndelRealigner automatically Left Aligns the Indels and so there will be no need to call LeftAlignIndels explicitly. However after reading the link in your post I realise that there is no functional overlap between IndelRealigner and LeftAlignIndels.

    Thx for your help.


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