hello,
I have a question regarding the quality and functionality of mutect v2 because I encountered some problem with data analysis when using mutect v2 versus mutect v1.
In fact, I am analysing whole-genome sequencing data from rat tumours. I first used mutect and mutect v2 using default settings.
the results were quite weird:
Mutect 1 gave me only 1,000 SNV with an allelic frequency ranging between 20 and 70%. whereas mutect v2 gave me 26,000 SNV with an allelic frequency <20% !
can you please explain to me the problem here? and how can it be fixed ?
Many thanks,
Best,