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.
Why GATK3.3 gives a more number (almost double) of INDELs than SNPs ?
I am working on Rice to call variants using GATK3.3. I have used BWA (bwa mem -M options) to map reads to reference genome. Followed by variant calling (HaplotypeCaller) by following Best Practices of GATK3.3. I have compared the results of 20 genotypes and in all genotypes INDELs are more (2x) as compared to SNPs. Please suggest me on this