I know there are some good homozygous calls in this VCF, yet vcf-tools can not see them for whatever reason. Any filtering for MAF or alt read count results in total elimination of all 1/1 homozygous calls.

an example VCF row:

chr3    69313555    rs1483895   C   T   222 .   AC1=2;AC=4;AF1=1;AN=4;ANN=T|intron_variant|MODIFIER|FRMD4B|FRMD4B|transcript|XM_017005989.1|protein_coding|1/23|c.163-38G>A||||||,T|intron_variant|MODIFIER|FRMD4B|FRMD4B|transcript|NM_015123.2|protein_coding|1/22|c.163-38G>A||||||,T|intron_variant|MODIFIER|FRMD4B|FRMD4B|transcript|XM_017005992.1|protein_coding|1/23|c.1-38G>A||||||,T|intron_variant|MODIFIER|FRMD4B|FRMD4B|transcript|XM_017005994.1|protein_coding|1/22|c.1-38G>A||||||,T|intron_variant|MODIFIER|FRMD4B|FRMD4B|transcript|XM_005264722.1|protein_coding|1/22|c.28-38G>A||||||,T|intron_variant|MODIFIER|FRMD4B|FRMD4B|transcript|XM_017005990.1|protein_coding|1/23|c.28-38G>A||||||,T|intron_variant|MODIFIER|FRMD4B|FRMD4B|transcript|XM_017005993.1|protein_coding|1/22|c.1-38G>A||||||,T|intron_variant|MODIFIER|FRMD4B|FRMD4B|transcript|XM_017005991.1|protein_coding|2/24|c.1-38G>A||||||;ASP;CAF=0.393,0.607;COMMON=1;DP4=0,0,4,30;DP=36;FQ=-77.9863;G5;G5A;GENEINFO=FRMD4B:23150;GNO;HD;INT;KGPhase1;KGPhase3;MQ0F=0;MQ=60;MQSB=1;RS=1483895;RSPOS=69313555;RV;SAO=0;SF=0,1;SGB=-0.690438;SLO;SSR=0;TOPMED=0.394567,0.605433;VC=SNV;VDB=0.0219339;VLD;VP=0x05010008000517053f000100;WGT=1;dbSNPBuildID=88  GT:DP:PL    1/1:17:255,51,0 1/1:17:255,51,0

please note the duplicate GT:DP:PL fields at the end. This may be a problem.

command:

vcftools --vcf my.vcf  --minDP 5 --minQ 30 --maf 0.00001 --remove-indels --recode --recode-INFO-all -c | grep '1/1:'

... nothing

EDIT:

The duplicate last column was not the problem, I removed it and got the same result. This problem occurs with both --maf and --mac > 0. --mac 0 returns rows, --mac 1 returns none.