Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.

Question about GATK4 SplitNCigarReads tool

Hi, I used the GATK SplitNCigarReads tools to process RNA-Seq data, which is said to reduce the false positive rate. Then, the processed data was used for SNP calling(by using variant calling tools in GATK). However, after annotating the SNP calling result with GTF file. It shows that only 20%~30% SNP sites locate in the exonic region. I was wonder about it. Ideally, most of the SNP sites may locate in the exonic region. Could u please help me solve this puzzle?


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @hubs

    This forum deals with questions related to GATK tools specific questions. Your question is more regarding your dataset. Your question will be better suited in www.biostar.org or www.seqanswers.com

  • hubshubs Member
    I do not think it caused by my dataset. It just an RNA MeRIP-Seq INPUT sample which can be regarded as RNA-Seq data. Just use the RNA-Seq SNP calling method supported by 'Calling variants in RNAseq' in this forum. However, the result is not satisfactory.
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin


    You see this % because there's probably reads outside of the exon. You could filter things outside of the exon out if they don't expect them. Or not call over those regions in the first place.
    SplitNCigarReads doesn't move the alignments, just splits them, so if their aligner put a bunch of reads in non-exonic regions, haplotypecaller (or Mutect) will call in those regions
    I hope this helps.

Sign In or Register to comment.