GATK-HaplotypeCaller results generate records with read depth of zero?

Question

[xie186]

GATK version used: GATK/4.1.4.1

Exact GATK commands used:

gatk HaplotypeCaller -R Pfalciparum.genome.fasta -I recal_realn.bam -ploidy 2 -ERC GVCF --standard-min-confidence-threshold-for-calling 30.0 -O HapoCaller.raw.g.vcf

I found that "DP" of some of the positions are ZEROs (e.g. the one shown below).

Pf3D7_07_v3 777185 . T *,A,<non_ref> 38.86 . DP=6;ExcessHet=3.0103;MLEAC=0,2,0;MLEAF=0.00,1.00,0.00;RAW_MQandDP=21600,6 GT:AD:DP:GQ:PL:SB 2/2:0,0,0,0:0:9:162,22,109,13,9,0,102,75,20,136:0,0,0,0

Could anyone please tell me why DP is ZERO in "2/2:0,0,0,0:0:9:162,22,109,13,9,0,102,75,20,136:0,0,0,0"? Thanks.

Answer 1

[Pierre Lindenbaum]

It's a GVCF, not a what-you-expect-to-be-a-VCF. https://gatkforums.broadinstitute.org/gatk/discussion/4017/what-is-a-gvcf-and-how-is-it-different-from-a-regular-vcf

it must be followed by GenotypeGVCF

[xie186]

Thanks for the link. In the vcf I got by GenotypeGVCFs. I was give

Pf3D7_07_v3     777185  .       T       A       30.05   PASS    AC=2;AF=0.016;AN=124;DP=1076;ExcessHet=0.0207;FS=0.000;InbreedingCoeff=0.3891;MLEAC=2;MLEAF=0.016;MQ=60.00;SOR=0.693;VQSLOD=5.75;culprit=FS;EFF=UPSTREAM(MODIFIER||1921||PF3D7_0717900|protein_coding|CODING|PF3D7_0717900.1|)  GT:AD:DP:GQ:PL     1/1:0,0:0:13:162,13,0  ..........................................................................................

I have more than 50 samples. I only showed the info for the sample I have question with. You can see here. The genotype information was given but the DP info is still zero.