Miscalling of SNPs and GQ value of 0

[Sgornard]

Problem report

Affected tool(s) or class(es)

HaplotypeCaller

Affected version : 4.1

Description

We used gatk HaplotypeCaller to find SNPs in our samples, following this command line:
gatk HaplotypeCaller --java-options "-Xmx20g -XX:ParallelGCThreads=10" -R ref_genome.fa -I sample.bam -ERC GVCF -O output_sample.g.vcf.gz

Afterward, we also used GenomicsDBImport, GenotypeGVCFs and VariantFiltration.

However, we noticed quickly some genotypes had a GQ tag equal to 0 despite a very good DP. Looking at the PL, it seemed like gatk could not decide between a homozygous and a heterozygous site, but still called a homozygous site and displayed all reads mapping to the reference allele. Looking at the read mapping in IGV, we noticed that those sites were in fact heterozygous, and therefore miscalled.

Here is an example (we could provide more if needed) :
Site :

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									ZCh209E	ZCh210C	ZCh212C	ZChGA78441	ZChGA78478	ZChGA78479	ZChGA78481	ZChGA78483	ZChGA78529
Chr2	136076952	.	C	G	29209.6	PASS	AC=13;AF=0.952;AN=18;BaseQRankSum=0;DP=881;ExcessHet=0.2205;FS=0;InbreedingCoeff=0.4627;MLEAC=167;MLEAF=1;MQ=59.06;MQRankSum=0;QD=30.27;ReadPosRankSum=1.91;SOR=0.714	GT:AD:DP:GQ:PGT:PID:PL:PS	1/1:6,30:36:46:.:.:1036,46,0:.	0/0:35,0:35:0:.:.:0,0,209:.	0/1:12,15:27:99:.:.:545,0,408:.	0/1:17,11:28:99:.:.:360,0,438:.	1/1:3,23:26:53:.:.:846,53,0:.	1/1:0,32:32:96:.:.:1325,96,0:.	1/1:5,21:26:14:.:.:710,14,0:.	0/1:9,16:25:99:.:.:593,0,301:.	1/1:0,23:23:69:.:.:949,69,0:.

Here, genotype of the individual ZCh210C is said to be homozygous (GT 0/0) and have all reads mapping the reference allele (AD 35:0). The GQ is 0, and PL is 0 for both homozygous and heterozygous genotypes.
The reads in IGV for this individual map as follows:

Which clearly shows reads mapping on the alternative allele.

Why is gatk having this behavior?

Thank you for your anwsers,
Best,

Samuel

[gokalpcelik]

Have you tried with a recent version such as 4.6.1.0? 4.1 is quite old and it has been a long time since then.