I've called my samples with HapltypeCaller in GVCF mode, and then jointly called variants with GenotypeGVCFs. I've included a variant below. As you see, one sample is called homozygous reference 0/0, while another is a no-call ./..
chr1 11722829 rs6540990 C T 86.90 PASS AC=2;AF=0.500;AN=4;ANN=T|downstream_gene_variant|MODIFIER|DRAXIN|DRAXIN|transcript|NM_198545.3|protein_coding||c.*3133C>T|||||2550|,T|intergenic_region|MODIFIER|DRAXIN-AGTRAP|DRAXIN-AGTRAP|intergenic_region|DRAXIN-AGTRAP|||n.11722829C>T||||||;DB;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;PG=0,0,0;QD=28.97;SOR=1.022;VQSLOD=19.48;culprit=MQ GT:AD:DP:GQ:PL:PP 1/1:0,3:3:9:99,9,0:99,9,0 0/0:4,0:4:0:0,0,0:0,0,0 ./.:0,0
One annoying thing with the no-call is that I don't get any annotations, like depth, as I do with the hom.ref. call. Another problem is that it isn't even taken into account in the INFO field as well, so the allele frequency is AF=0.500, while it should probably be AF=0.333, assuming the genotype should be 0/0.
Why was one sample not called while another got a hom.ref. call? Is there any way I can force a call?