To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

how to determine whether the variants is true by the IGV alignment views ?

how to determine whether the variants is true by the IGV alignment views ?
is there a good paper to introduce that ?




  • shleeshlee CambridgeMember, Broadie, Moderator
    edited May 2017

    Hi @YingLiu, I'm not aware of any paper but we haven't actively searched for such. Let me check with the IGV team.

    In the meanwhile, note that many of the artifactual alignments in variant calling are alluded to by GATK read filters as well as IGV color by (sort by, etc) options (see the Alignment Track section here).

    We have plans to illustrate a number of MuTect2 called and filtered sites as a tutorial on the forum. I will be getting to this sometime this year. However, manual review of variants can be tricky even for experienced genomicists. So tricky that our developers have a bi-monthly meeting to review variant calls that involves using alignments from different technologies.

  • bioggrimesbioggrimes EdinburghMember

    This paper has some good advice for manual review of variants using IGV.

    Standard operating procedure for somatic variant refinement of tumor sequencing data

  • SheilaSheila Broad InstituteMember, Broadie, Moderator


    Thank you for sharing this :smile:


Sign In or Register to comment.