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.
Mutect2 Amplicon realigment behavior
i was playing around with mutect2 and amplicons. I follow the best practise and run mutect2 with the following commands:
$java7Path\java -Xmx4g -jar $gatkPath\
-T MuTect2 \
-R $referencePath \
-I:tumor $I \
-dt NONE \
When i view the results a noticed that a evident call from the UG was missing in the mutect output. After i saw the bamOut from mutect, I release why... after the realignment all reads from the position were removed.
Here a view of both bam in igv: