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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

SNP call by GATK is quite different from the eye observation in IGV

Hi All,

I have a question regarding the SNP call by GATK3.2 vs the eye observation in IGV; both use hg19:
We have three samples, in the IGV, I see the following genotypes from BAM file (after realign and recalibration; before HaplotypeCaller):
Sample 1: 9Gs and 11Ts
Sample 2: 6Gs and 6Ts
Sample 3: 18Gs

But when I check the vcf produced by GATK, it shows:
chr10 17659149 rs7895850 C G,T 1509.20 PASS AC=4,2;AF=0.667,0.333;AN=6;DB;DP=41;FS=0.000;MLEAC=4,2;MLEAF=0.667,0.333;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.48;VQSLOD=6.71;culprit=MQ GT:AD:DP:GQ:PL 1/1:0,14,0:14:41:493,41,0,493,41,493 2/2:0,11,0:11:33:429,429,429,33,33,0 1/1:0,16,0:16:48:704,48,0,704,48,704

If you look at the GT field, the corresponding genotypes are sample1 as G, sample2 as T, sample3 as G.
They are quite different from the IGV for sample 1 and 2.
I am wondering if you have any idea about this?



Sign In or Register to comment.