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.

Merging adjavent SNPs into MNPs.

nirucgnirucg Cambridge MAMember

I have many adjacent SNPs in my VCF that I need to merge into MNP. These SNPs can be homozygous or heterozygous.
For example:
chr1 889158 rs13303056 G C
chr1 889159 rs13302945 A C
The two SNPs above need to be turned into the MNP below:
chr1 889158 . GA CC

I tried the option --mergeVariantsViaLD in HaplotypeCaller but as mentioned in other posts, it didn't really work.

What are my options for merging?

Thanks.

Tagged:

Best Answer

Answers

Sign In or Register to comment.