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Possible to Merge Deletion and SNP event with MNP or Another Tool

afontanaafontana Member
I am trying to call a deletion SNP using MuTect2 from GATK4.1.2 and am following best practices. This is a common mutations in LUAD. I have attached the IGV Screenshot here. This seems unrelated to the MNP Dist length I provide to MuTect2. This is WES.

With MNP:
chr7 55242465 . GGAATTAAGA G . PASS
chr7 55242475 . GAAG CAAC . PASS

Without MNP:
BRAIN26 - With No MNP Merge
chr7 55242465 . GGAATTAAGA G . clustered_events;haplotype
chr7 55242475 . G C . clustered_events;haplotype
chr7 55242478 . G C . clustered_events;haplotype

Is there a way to have this be a single call? Or is there a way to merge the calls in post-processing?

I am aiming for an annotations which would produce L747_A750delinsP after annotation.
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