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.

allele depth is conflicting with reads depth

Hi,

I checked the vcf file to get the depth for each allele. for example this allele:

scaffold44 2127674 . T C 106064.77 PASS AC=2;AF=1.00;AN=2;DP=2220;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.42;SOR=6.305 GT:AD:DP:GQ:PL 1/1:0,2220:2220:99:106093,7101,0

it means there are 2220 reads cover it, and all of them are ALT alleles. But I checked the reads depth from IGV, the real depth is 713091. Why are they different?

Thank you very much~

Tagged:

Answers

Sign In or Register to comment.