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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?



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