Varinat PASS given Genotype quality = 0

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Matteo Orlandi

• November 14, 2022 14:05

REQUIRED for all errors and issues:
a) GATK version used: 4.3.0.0

Hi,

I am using GATK HC on a single sample (in the context of a pipeline) with the following command: $gatk HaplotypeCaller -R $FASTA -I $id/$bam -ERC GVCF --output $tempGvcf/$id.snps.raw.g.vcf.gz --standard-min-confidence-threshold-for-calling 30.0 --dont-use-soft-clipped-bases true --sample-ploidy $ploidy -bamout $id/${id}_HC_output.bam

Then, with GenotypeGVCFs I get the VCF: $gatk  GenotypeGVCFs -R $FASTA -V $tempGvcf/complete.g.vcf.gz -G StandardAnnotation -O $res/complete.raw.vcf.gz

What I am experiencing is that for some variants I can observe a genotype (e.g., 0/1) even if the Genotype quality is 0.

chr1    124935822    .    C    G    251.06    .    AC=1;AF=0.500;AN=2;BaseQRankSum=-1.260e-01;DP=10;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=48.09;MQRankSum=1.65;QD=25.11;ReadPosRankSum=1.65;SOR=1.022    GT:AD:DP:GQ:PL    0/1:1,9:10:0:258,0,0

Moreover, this variant is also reported as PASS when using either the VQSR filter or the hard-filters (GATK best practice). 

How is possible that a variant with GQ = 0 is PASS?

I've also checked the HC's bam and I can actually see that variant with frequency of 80%.

Thank you in advance.

 

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  Anthony DiCi

  • November 22, 2022 18:13

  Hi Matteo Orlandi,

  Thank you for writing to the GATK forum! I hope that we can help you sort this out.
  After reviewing your post with our developers, I have some feedback to share with you. 

  A variant with a GQ = 0 being PASS is not unexpected. It is clear that there is a variant here, but we won't be able to distinguish its genotype.

  While the mapping quality could be better, this is still a perfectly reasonable variant. Unfortunately, it doesn't have the best allele balance, so we can't tell what the genotype is but this is as expected.

  I hope this helps clear some of your doubts! Thank you again for writing to the GATK forum. Please do not hesitate to reach out if any further questions should arise.

  Best,
  Anthony

   

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  Anthony DiCi

  • November 30, 2022 16:27

  Hi Matteo Orlandi,

  We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

  Kind regards,

  Anthony​

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