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.
Attention:
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

Using dbSNPs for mapping

kellermackellermac Baton Rouge, LouisianaMember

Hi. So I want to take a dbSNP file and highlight SNPs that are found in some BAM files. Instead of filtering these I want to search for these SNPs only. I will then use these SNP positions as markers to trace recombination events that have occured between some strains I am studying. So far I havn't found a good strategy to accomplish this. I was hoping someone over here knows how to parse the dbSNP, and could guide me through it. Alternatively you could use this idea to generate a new tool! Please let me know if you have thoughts, or questions. Thanks! -Keller

Tagged:

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin

    Hi Keller, I'm not sure I understand exactly what you want to do, but in general it sounds like something that should be possible with GATK. For example if you have a VCF file containing variants of interest, and you just want to select those that are present in dbSNP, that is very easy using the GATK tool SelectVariants.

    Can you please clarify what data you have available and exactly what you would like to produce?

Sign In or Register to comment.