If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.

if two variant are side by side,will gatk try to merge them?

hi, image there is A -> T in position 2, and A -> G in position 3 or A -> NONE ,
will gatk try to merge(the combination can be snp+snp, snp+indel, indel+indel), because different combination or single alone can generate a totally different amino change, and finaly impact the drug instruction.

VarScan will merge some variants if it think ok, but also give single alone variant

Sign In or Register to comment.