Service notice: Several of our team members are on vacation so service will be slow through at least July 13th, possibly longer depending on how much backlog accumulates during that time. This means that for a while it may take us more time than usual to answer your questions. Thank you for your patience.

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

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

Best

Tagged:

Answers

  • 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

    https://www.biorxiv.org/content/early/2018/02/21/266262

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @bioggrimes
    Hi,

    Thank you for sharing this :smile:

    -Sheila

Sign In or Register to comment.