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.
Variant reported by GATK is not seen in IGV
I am facing an issue with GATK 3.8. After running GATK HaplotypeCaller I get one variant detected as
Pf3D7_05_v3 133207 . A G 60 . AC=1;AF=1.00;AN=1;DP=2;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=30.00;SOR=0.693 GT:AD:DP:GQ:PL 1:0,2:2:90:90,0
but when i see it in IGV it does not show any such variant detected there and show the reference allele. Can anyone please help me why it is so?