No quality in non-variant sites

[gubrins]

Heys,

I am doing the SNP calling with Haplotypecaller BP_Resolution, CombineGVCFs with convert-to-base-pair-resolution and GenotypeGVCFs with include-non-variant-sites with GATK v.4.1.7.0 and when I get my vcf file, the non-variant sites does not have any quality at all:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  Leopards_1  Leopards_2
NC_001700.1 1   .   G   .   .   .   DP=40   GT:AD:DP:RGQ    0/0:26:26:78    0/0:14:14:42
NC_001700.1 2   .   G   .   .   .   DP=43   GT:AD:DP:RGQ    0/0:29:29:87    0/0:14:14:42
NC_001700.1 3   .   A   .   .   .   DP=43   GT:AD:DP:RGQ    ./.:0:29:0  ./.:0:14:0
NC_001700.1 4   .   C   .   .   .   DP=43   GT:AD:DP:RGQ    ./.:0:29:0  ./.:0:14:0
NC_001700.1 5   .   T   .   .   .   DP=71   GT:AD:DP:RGQ    0/0:50:50:99    0/0:21:21:63
NC_001700.1 6   .   A   .   .   .   DP=74   GT:AD:DP:RGQ    0/0:53:53:99    0/0:21:21:63
NC_001700.1 7   .   A   .   .   .   DP=85   GT:AD:DP:RGQ    0/0:59:59:99    0/0:26:26:78

Except for the variant ones:

NC_001700.1 63  .   T   A   6198.13 .   AC=4;AF=1.00;AN=4;DP=252;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=48.90;QD=24.60;SOR=0.709   GT:AD:DP:GQ:PL  1/1:0,166:166:99:4057,496,0 1/1:0,86:86:99:2157,258,0

Do you know what is this happening?

[gubrins]

So I tried with gatk v.4.1.3.0 and the quality parameters appear. Is this a version problem? I also tried with the newest one and it did not work

[krukanna]

Hey, I've the same problem. In version 4.1.3.0 and 4.1.4.0 the quality value appear. In the latest version 4.2.6.1 don't have QUAL value, only dot.

GenotypeGVCFs Version="4.1.3.0"
chr1    69973   .   A   .   23.89   LowQual DP=1131 GT:AD:DP:RGQ     0/0:26,0:26:72 0/0:34,0:34:102  0/0:12,0:12:36
GenotypeGVCFs Version="4.2.6.1"
chr1    69973   .   A   .   .   .   DP=1131 GT:DP:RGQ   0/0:26:72   0/0:34:99   0/0:12:36

In latest version missing fields are QUAL, AD and RGQ is always truncated to 99 (if greater).