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SNP calling for heterozygosity and homozygosity

I have a question about SNP calling from GATK.

We want to call the SNP from many individuals. We hope that we could have the right confident Genotype SNP. But when I check the SNP results, I find some problem, such as the following example:

scaffold_1 12816 . C T 5075.21 TruthSensitivityTranche99.90to100.00 AC=20;AF=0.417;AN=48;BaseQRankSum=14.475;DB;DP=2186;Dels=0.00;FS=1.453;HRun=1;HaplotypeScore=1.2508;InbreedingCoeff=0.8258;MQ=23.69;MQ0=948;MQRankSum=-11.287;QD=10.78;ReadPosRankSum=13.705;SB=-276.66;VQSLOD=-17.8239;culprit=ReadPosRankSum
GT:AD:DP:GQ:PL
0/0:204,0:204:99:0,366,3726 **1/1:19,20:39:27.03:249,27,0 ** 0/0:110,0:110:99:0,219,2229 0/1:54,20:74:27.15:27,0,871 0/0:98,0:98:99:0,156,1701 0/0:208,0:211:99:0,490,5141 0/0:147,0:148:99:0,279,2915 ./. 1/1:6,22:28:27.04:282,27,0 1/1:0,31:31:39.04:360,39,0 0/0:220,0:220:99:0,424,4397 ./. 1/1:0,30:30:75.07:692,75,0 0/1:25,12:37:99:101,0,637 1/1:0,36:36:69.07:636,69,0 0/0:39,0:39:87.10:0,87,852 1/1:23,61:84:99:1107,120,0 1/1:0,38:38:78.08:736,78,0 ./. ./. 0/0:131,0:131:99:0,213,2230 1/1:6,37:43:57.08:593,57,0 1/1:12,19:31:30.04:293,30,0 0/0:27,8:35:54.08:0,54,537 ./. 0/0:64,0:65:96.13:0,96,993 0/0:116,1:117:99:0,207,2124 ./. 0/0:5,0:5:15.03:0,15,162 0/0:95,0:95:99:0,192,2012

I have 30 individuals that need to call the SNPs. I find that GT are different based on the reads depth. for one individual: 1/1:19,20:39:27.03:249,27,0. The two alleles are covered by 19 and 20 reades, the Genotype should be 0/1 as a heterozygosity. but GATK call it as a homozygosity. What is the problem?

There are lots of this situation in my data. How can I make sure the GATK's SNP are right or wrong? Hope you can give me some help?

Best
Zhiqiang

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Answers

  • wuzhiqiangwuzhiqiang LubbockMember

    Yes. Our lab just updata the GATK on this May. (The Genome Analysis Toolkit (GATK) v2.4-9-g532efad, Compiled 2013/03/19 07:35:36
    ).
    Your suggestion is good. I think that I should combined with GQ and PL to call the confident SNP.
    Thanks!
    zhiqiang

  • wuzhiqiangwuzhiqiang LubbockMember

    Thanks! I will update our version.
    Best
    Zhiqiang

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