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!

# the number of reads of diploidy, triploidy and tetraploidy

SouthKoreaMember

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?

0/1/2:35,3,14:0.069,0.275:13,2,6:22,1,8:31,30:149,197,147:60,60:42,43:0.253,0.232,0.269:0.029,0.014,0.957

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!

Tagged:

• MunichMember ✭✭✭

Hi,

it's not really triploidy or tetraploidy.
If you have a few different subclones in your tumor, each of them might be diploid for a chromosome or n-ploid, but a specific position can be different or the same in each clone.
For example let's say you have 4 clones in your sample. Each of them has two copies if chromosome 1 and is therefore dipoid. At position 1000 there is an A in reference. One sublone might have an A, one has a C and two have a G. This will result in 3 different alleles even though every clone is diploid. If your sample contains roughly the same amount of DNA from each clone, you will see something like 0/1/2:10,10,20[....], but if you have one clone overrepresented in your sample, the allelic depths can be completely different.

But your assumption is correct. If you just want to now the number of alt reads, you can just add 3+14.

Best,
Daniel