The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!


You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

SNP calling for heterozygosity and homozygosity

wuzhiqiangwuzhiqiang LubbockMember Posts: 3

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

Tagged:

Best Answers

Answers

  • wuzhiqiangwuzhiqiang LubbockMember Posts: 3

    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 Posts: 3

    Thanks! I will update our version.
    Best
    Zhiqiang

Sign In or Register to comment.