Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

the number of reads of diploidy, triploidy and tetraploidy

suhyesuhye 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:

Answers

  • dbeckerdbecker 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

Sign In or Register to comment.