Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Is it useful to call LeftAlignIndels after IndelRealigner

ambi1999ambi1999 United KingdomMember

Hi,

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.

Cheers,
Ambi.

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @ambi1999
    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.

    -Sheila

  • 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.

    Cheers,
    Ambi.

Sign In or Register to comment.