We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

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

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.

Best Answer


Sign In or Register to comment.