how to determine whether the variants is true by the IGV alignment views ?
is there a good paper to introduce that ?
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.
This paper has some good advice for manual review of variants using IGV.
Standard operating procedure for somatic variant refinement of tumor sequencing data
Thank you for sharing this