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.
Location of variant in multi-sample calling
While using your best practices pipeline, using multisample calling, I get these multi-allelic variants. As I am interested in the precise position of certain variants, I would like to know if there is a way to identify, where a variant is located. This is ofcause possible in most cases, but I have a subset of my variants, where I cannot see how this can be done
Examples from my VCF-file:
17 8045028 . CTTTTTTCTCCCCCTTGAACTTGAGCTCAATTCT CTTTTTCTCCCCCTTGAACTTGAGCTCAATTCT,C
9 32986030 . TAAAAAAAAAACAAAAAAAAAAAC TAAAAAAAAACAAAAAAAAAAAC,TAAAAAAAAAC,T,AAAAAAAAAAACAAAAAAAAAAAC
In the first example, I cannot see which "T" has been deleted - this could be any of them:
In the second example, I cannot see which "A" has been deleted:
Is there any way, I can get information on which one it is?