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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: