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.

How to handle consecutive indels?

Kelly135Kelly135 KoreaMember
edited May 2017 in Ask the GATK team

Hi all,

I have one question regarding indels in vcf.
Here is an example of consecutive indels from vcf file.

chr pos ref alt
chr1 218616012 TTC T,*
chr1 218616013 TC T,*

I believe, these two indels are same.

to visualize one genotype of first variant with the first alt allele T
pos 12 13 14
ref T T C
alt T - -

second variant with the second alt allele *
pos 12 13 14
ref T T C
alt T - -

I found several problems regarding these consecutive indels, so I ran "vt normalize" with this file, but there were no variants normalized from this process. So, what should I do with this sort of variants? I don't think these are independent variants.
FYI, I made vcfs through the process of best practice.

Any comment will help. Thanks always.

Best Answer


Sign In or Register to comment.