the number of reads of diploidy, triploidy and tetraploidy
Hello, I'm suhye from southkorea
I usually used GATK4 tools for analysis my data! thanks
When i used GATK4-Mutect2 tool for somatic mutation calling,
I have got some questions of this tool.
In Genotype column, I could find 0/1/2 , 0/1/2/3 or 0/1/2/3/4 instead of 0/1. this call means diplody, triploidy. . . right?
So how can I get the number of alternated read?
In this call, Can i get the number of alternated read by just adding (3+14)?
as i know, 35 means the number of reference allele reads.
Thanks, GATK team!