Gatk Hardyweinberg Calculation

Question

[mark.dunning]

Hi all,

I am trying to do a Hardy-Weinberg test on my raw GATk calls as part of my filtering to remove false positives. This is the call I am using;

java -jar software/GATK/GenomeAnalysisTK-1.6-13-g91f02df/GenomeAnalysisTK.jar -T VariantAnnotator --variant GATK.raw.snps.vcf -R homo_sapiens.fa -A HardyWeinberg --out HW.vcf

In the resulting vcf file, the HW flag appears in the header

But none of the SNPs have HW in the INFO

chr1    13012    .    G    A    85.54    .    AC=4;AF=0.333;AN=12;BaseQRankSum=-9.827;DP=903;DS;Dels=0.00;FS
=0.000;HRun=0;HaplotypeScore=2.5501;MQ=12.73;MQ0=336;MQRankSum=-0.000;QD=0.15;ReadPosRankSum=-0.022;SB=-51.55    GT:AD:
DP:GQ:PL    0/1:118,28:146:35.15:35,0,141    0/1:130,19:151:24.58:25,0,280    0/1:156,34:190:33.56:34,0,503    0/1:61
,10:71:43.10:43,0,239    0/0:88,7:95:20.98:0,21,232    0/0:211,36:250:43.14:0,43,566

Any idea why the HW value is not appearing?

Regards,

Mark

Answer 1

[Brad Chapman]

The HardyWeinberg annotator needs at least 10 samples to output the score:

HardyWeinberg Java source at GitHub

so you'll need to merge in a few additional samples to reliably calculate this metric.

[mark.dunning]

Many thanks for the information. I would have be nice if GATK had informed me of that when I tried to run it....