I was wondering for other people's opinion about the accuracy of MuTect2 regarding INDEL's detection.Are you satisfied?
No pitfall behind that, just wondering!!
Thank u in advance!
It's a fair question, and we'd love to get some feedback from the community on this.
Hi, I used mutect2 indel to call indel varaints and got some long insertions of more than 50 bp. I inspected the varaint with IGV, but got no reads with inserted bases, why? Beaside, I checked the varaint with samtools tview in bam file, also no reads were inserted with those bases. This confused me a lot, please help me with this problem.
Have you checked the bamout?