If the genotype filter was applied to at least one of samples only then the FT Tag is added to the output vcf. This is done in order to determine which sample "PASS" filter and which sample didn't.

Example user error:

A couple of variants for only 5/95 samples from the input vcf (APOE.recode.genotypeRefined.vcf) are shown below:

chr19 44907654 rs769451 T G 1131.52 PASS AC=3;AF=0.016;AN=190;BaseQRankSum=-4.920e-01;DB;DP=2959;ExcessHet=3.0798;FS=0.788;InbreedingCoeff=-0.0160;MLEAC=3;MLEAF=0.016;MQ=59.93;MQRankSum=0.00;PG=0,16,39;POSITIVETRAINSITE;QD=12.04;ReadPosRankSum=0.00;SOR=0.582;VQSLOD=9.43;culprit=MQRankSum GT:AD:DP:GQ:PL:PP 0/0:37,0:37:99:0,99,1485:0,115,1524 0/0:35,0:35:99:0,99,1485:0,115,1524 0/0:27,0:27:85:0,69,1035:0,85,1074 0/0:37,0:37:99:0,99,1485:0,115,1524 0/0:25,0:25:82:0,66,990:0,82,1029

chr19 44908684 rs429358 T C 4672.69 PASS AC=24;AF=0.126;AN=190;BaseQRankSum=-2.469e+00;DB;DP=1958;ExcessHet=4.7065;FS=1.755;InbreedingCoeff=-0.0544;MLEAC=24;MLEAF=0.126;MQ=59.98;MQRankSum=0.00;PG=0,10,26;POSITIVETRAINSITE;QD=9.40;ReadPosRankSum=0.283;SOR=0.859;VQSLOD=8.99;culprit=MQRankSum GT:AD:DP:GQ:PL:PP 0/1:27,4:31:28:38,0,909:28,0,925 0/0:29,0:29:94:0,84,1260:0,94,1286 0/0:15,0:15:55:0,45,563:0,55,589 0/0:19,0:19:67:0,57,694:0,67,7200/0:10,0:10:40:0,30,302:0,40,328

I ran the following command: /usr/bin/java -jar gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar VariantFiltration --variant APOE.recode.genotypeRefined.vcf --genotype-filter-expression "GQ < 20" --genotype-filter-name "lowGQ" --output APOE.recode.genotypeRefined.filteredoutLowGQ.vcf

The output for the above two variants is shown below:

chr19 44907654 rs769451 T G 1131.52 PASS AC=3;AF=0.016;AN=190;BaseQRankSum=-4.920e-01;DB;DP=2959;ExcessHet=3.0798;FS=0.788;InbreedingCoeff=-0.0160;MLEAC=3;MLEAF=0.016;MQ=59.93;MQRankSum=0.00;PG=0,16,39;POSITIVETRAINSITE;QD=12.04;ReadPosRankSum=0.00;SOR=0.582;VQSLOD=9.43;culprit=MQRankSum GT:AD:DP:GQ:PL:PP 0/0:37,0:37:99:0,99,1485:0,115,1524 0/0:35,0:35:99:0,99,1485:0,115,1524 0/0:27,0:27:85:0,69,1035:0,85,1074 0/0:37,0:37:99:0,99,1485:0,115,1524 0/0:25,0:25:82:0,66,990:0,82,1029

chr19 44908684 rs429358 T C 4672.69 PASS AC=24;AF=0.126;AN=190;BaseQRankSum=-2.469e+00;DB;DP=1958;ExcessHet=4.7065;FS=1.755;InbreedingCoeff=-0.0544;MLEAC=24;MLEAF=0.126;MQ=59.98;MQRankSum=0.00;PG=0,10,26;POSITIVETRAINSITE;QD=9.40;ReadPosRankSum=0.283;SOR=0.859;VQSLOD=8.99;culprit=MQRankSum GT:AD:DP:FT:GQ:PL:PP 0/1:27,4:31:PASS:28:38,0,909:28,0,925 0/0:29,0:29:PASS:94:0,84,1260:0,94,1286 0/0:15,0:15:PASS:55:0,45,563:0,55,589 0/0:19,0:19:PASS:67:0,57,694:0,67,720 0/0:10,0:10:PASS:40:0,30,302:0,40,328

The variant rs429358 has Genotype-level filter, FT tag for all the samples, while the variant rs769451 has no FT tag which means the genotype filter was not applied to this variant.